Upgrade Doxygen configuration files for Doxygen 1.8.1, fix broken stylesheet and footer HTML, add explicit spacing into documentation code fragments to prevent Doxygen from removing empty lines in the output.

git-svn-id: http://lufa-lib.googlecode.com/svn/trunk@2224 d5102386-fcda-11dd-9fdb-3debd5008f28

106 files changed, 1388 insertions, 1800 deletions

diff --git a/Bootloaders/CDC/BootloaderCDC.txt b/Bootloaders/CDC/BootloaderCDC.txt
index e88a7fba..a3f74f3e 100644
--- a/Bootloaders/CDC/BootloaderCDC.txt
+++ b/Bootloaders/CDC/BootloaderCDC.txt
@@ -98,7 +98,7 @@
  *  #define BOOTLOADER_API_TABLE_SIZE          32
  *  #define BOOTLOADER_API_TABLE_START         ((FLASHEND + 1UL) - BOOTLOADER_API_TABLE_SIZE)
  *  #define BOOTLOADER_API_CALL(Index)         (void*)((BOOTLOADER_API_TABLE_START + (Index * 2)) / 2)
- *
+ *  
  *  void    (*BootloaderAPI_ErasePage)(uint32_t Address)               = BOOTLOADER_API_CALL(0);
  *  void    (*BootloaderAPI_WritePage)(uint32_t Address)               = BOOTLOADER_API_CALL(1);
  *  void    (*BootloaderAPI_FillWord)(uint32_t Address, uint16_t Word) = BOOTLOADER_API_CALL(2);
@@ -106,13 +106,13 @@
  *  uint8_t (*BootloaderAPI_ReadFuse)(uint16_t Address)                = BOOTLOADER_API_CALL(4);
  *  uint8_t (*BootloaderAPI_ReadLock)(void)                            = BOOTLOADER_API_CALL(5);
  *  void    (*BootloaderAPI_WriteLock)(uint8_t LockBits)               = BOOTLOADER_API_CALL(6);
- *
+ *  
  *  #define BOOTLOADER_MAGIC_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 2))
  *  #define BOOTLOADER_MAGIC_SIGNATURE         0xDCFB
- *
+ *  
  *  #define BOOTLOADER_CLASS_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 4))
  *  #define BOOTLOADER_CDC_SIGNATURE           0xCDC1
- *
+ *  
  *  #define BOOTLOADER_ADDRESS_START           (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 8))
  *  #define BOOTLOADER_ADDRESS_LENGTH          4
  *  \endcode
diff --git a/Bootloaders/CDC/Doxygen.conf b/Bootloaders/CDC/Doxygen.conf
index b03ff0bc..ea21cd05 100644
--- a/Bootloaders/CDC/Doxygen.conf
+++ b/Bootloaders/CDC/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - CDC Class Bootloader"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Bootloaders/DFU/BootloaderDFU.txt b/Bootloaders/DFU/BootloaderDFU.txt
index 13dd05b6..a01b1d9f 100644
--- a/Bootloaders/DFU/BootloaderDFU.txt
+++ b/Bootloaders/DFU/BootloaderDFU.txt
@@ -103,7 +103,7 @@
  *  #define BOOTLOADER_API_TABLE_SIZE          32
  *  #define BOOTLOADER_API_TABLE_START         ((FLASHEND + 1UL) - BOOTLOADER_API_TABLE_SIZE)
  *  #define BOOTLOADER_API_CALL(Index)         (void*)((BOOTLOADER_API_TABLE_START + (Index * 2)) / 2)
- *
+ *  
  *  void    (*BootloaderAPI_ErasePage)(uint32_t Address)               = BOOTLOADER_API_CALL(0);
  *  void    (*BootloaderAPI_WritePage)(uint32_t Address)               = BOOTLOADER_API_CALL(1);
  *  void    (*BootloaderAPI_FillWord)(uint32_t Address, uint16_t Word) = BOOTLOADER_API_CALL(2);
@@ -111,13 +111,13 @@
  *  uint8_t (*BootloaderAPI_ReadFuse)(uint16_t Address)                = BOOTLOADER_API_CALL(4);
  *  uint8_t (*BootloaderAPI_ReadLock)(void)                            = BOOTLOADER_API_CALL(5);
  *  void    (*BootloaderAPI_WriteLock)(uint8_t LockBits)               = BOOTLOADER_API_CALL(6);
- *
+ *  
  *  #define BOOTLOADER_MAGIC_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 2))
  *  #define BOOTLOADER_MAGIC_SIGNATURE         0xDCFB
- *
+ *  
  *  #define BOOTLOADER_CLASS_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 4))
  *  #define BOOTLOADER_CDC_SIGNATURE           0xDFB1
- *
+ *  
  *  #define BOOTLOADER_ADDRESS_START           (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 8))
  *  #define BOOTLOADER_ADDRESS_LENGTH          4
  *  \endcode
diff --git a/Bootloaders/DFU/Doxygen.conf b/Bootloaders/DFU/Doxygen.conf
index 7739a7ed..9aec702f 100644
--- a/Bootloaders/DFU/Doxygen.conf
+++ b/Bootloaders/DFU/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - DFU Class Bootloader"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Bootloaders/HID/Doxygen.conf b/Bootloaders/HID/Doxygen.conf
index bce70d62..5fe5a69b 100644
--- a/Bootloaders/HID/Doxygen.conf
+++ b/Bootloaders/HID/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - HID Class Bootloader"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -961,12 +955,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -975,6 +963,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1132,7 +1131,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1153,11 +1152,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1727,7 +1721,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/AudioInput/Doxygen.conf b/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
index 3d334597..d217aa44 100644
--- a/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
+++ b/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf b/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
index 392086e9..4cd9e9c5 100644
--- a/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
+++ b/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf b/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf
index 3c9c10e2..0f78680c 100644
--- a/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf
+++ b/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Dual Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/GenericHID/Doxygen.conf b/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
index 78e4ff04..7b71c205 100644
--- a/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
+++ b/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Generic HID Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/Joystick/Doxygen.conf b/Demos/Device/ClassDriver/Joystick/Doxygen.conf
index 348faaf1..407d08a8 100644
--- a/Demos/Device/ClassDriver/Joystick/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Joystick/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/Keyboard/Doxygen.conf b/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
index 57095df3..0b47b1a3 100644
--- a/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf b/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
index 4016a2e4..a7357cb1 100644
--- a/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Keyboard/Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf b/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf
index b0ed4dc4..c3696bbd 100644
--- a/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf
+++ b/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Keyboard/Mouse (Multiple HID R
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/MIDI/Doxygen.conf b/Demos/Device/ClassDriver/MIDI/Doxygen.conf
index d17ed60c..f95325f8 100644
--- a/Demos/Device/ClassDriver/MIDI/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MIDI/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/MassStorage/Doxygen.conf b/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
index 9da2792a..4ef06750 100644
--- a/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf b/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf
index cf8be4ea..4f8b9e59 100644
--- a/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Mass Storage and Keyboard Devi
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/Mouse/Doxygen.conf b/Demos/Device/ClassDriver/Mouse/Doxygen.conf
index d92f7f63..1dd2ccd0 100644
--- a/Demos/Device/ClassDriver/Mouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Mouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf b/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
index 1da1f868..da74f6b4 100644
--- a/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
+++ b/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Ethernet Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf b/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf
index 2cd6e221..ebe72a5d 100644
--- a/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf
+++ b/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf b/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf
index c507f269..c38f51df 100644
--- a/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf
+++ b/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial/Mass Storage Device Demo
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf b/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf
index 6aaf9706..fea97b2d 100644
--- a/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Virtual Serial and Mouse Devic
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/AudioInput/Doxygen.conf b/Demos/Device/LowLevel/AudioInput/Doxygen.conf
index 3d334597..d217aa44 100644
--- a/Demos/Device/LowLevel/AudioInput/Doxygen.conf
+++ b/Demos/Device/LowLevel/AudioInput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/AudioOutput/Doxygen.conf b/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
index 392086e9..4cd9e9c5 100644
--- a/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
+++ b/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf b/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf
index 3c9c10e2..0f78680c 100644
--- a/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf
+++ b/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Dual Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/GenericHID/Doxygen.conf b/Demos/Device/LowLevel/GenericHID/Doxygen.conf
index 78e4ff04..7b71c205 100644
--- a/Demos/Device/LowLevel/GenericHID/Doxygen.conf
+++ b/Demos/Device/LowLevel/GenericHID/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Generic HID Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/Joystick/Doxygen.conf b/Demos/Device/LowLevel/Joystick/Doxygen.conf
index 348faaf1..407d08a8 100644
--- a/Demos/Device/LowLevel/Joystick/Doxygen.conf
+++ b/Demos/Device/LowLevel/Joystick/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/Keyboard/Doxygen.conf b/Demos/Device/LowLevel/Keyboard/Doxygen.conf
index 57095df3..0b47b1a3 100644
--- a/Demos/Device/LowLevel/Keyboard/Doxygen.conf
+++ b/Demos/Device/LowLevel/Keyboard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf b/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
index 4016a2e4..a7357cb1 100644
--- a/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
+++ b/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Keyboard/Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/MIDI/Doxygen.conf b/Demos/Device/LowLevel/MIDI/Doxygen.conf
index d17ed60c..f95325f8 100644
--- a/Demos/Device/LowLevel/MIDI/Doxygen.conf
+++ b/Demos/Device/LowLevel/MIDI/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/MassStorage/Doxygen.conf b/Demos/Device/LowLevel/MassStorage/Doxygen.conf
index 9da2792a..4ef06750 100644
--- a/Demos/Device/LowLevel/MassStorage/Doxygen.conf
+++ b/Demos/Device/LowLevel/MassStorage/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/Mouse/Doxygen.conf b/Demos/Device/LowLevel/Mouse/Doxygen.conf
index d92f7f63..1dd2ccd0 100644
--- a/Demos/Device/LowLevel/Mouse/Doxygen.conf
+++ b/Demos/Device/LowLevel/Mouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf b/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
index 1da1f868..da74f6b4 100644
--- a/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
+++ b/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Ethernet Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf b/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf
index 2cd6e221..ebe72a5d 100644
--- a/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf
+++ b/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf b/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf
index 8a3662e9..ec511fec 100644
--- a/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf
+++ b/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host/Device Dual Role Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf b/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf
index 7c75b522..36cb2f08 100644
--- a/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Android Accessory Mode Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf b/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf
index af07c395..f3ed928f 100644
--- a/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf b/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf
index 8255519a..237d312e 100644
--- a/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf b/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf
index c7c037a8..575abd0e 100644
--- a/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf
+++ b/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf b/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf
index 2557f330..e626e69b 100644
--- a/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf b/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf
index 00a850d3..72a0fb75 100644
--- a/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf
+++ b/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf b/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf
index 321cffdd..1d898aca 100644
--- a/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf b/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf
index 2522f53f..086bf674 100644
--- a/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MouseHost/Doxygen.conf b/Demos/Host/ClassDriver/MouseHost/Doxygen.conf
index 618c4d84..29459d8b 100644
--- a/Demos/Host/ClassDriver/MouseHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MouseHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf b/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf
index b2370b96..35b3dd06 100644
--- a/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo (Using HID Descriptor P
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf b/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf
index 791fe729..af83229f 100644
--- a/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Printer Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf b/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf
index 9b89a5da..8864c18d 100644
--- a/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Ethernet Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf b/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf
index 6341892c..f9ebf151 100644
--- a/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Still Image Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf b/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf
index 852d288b..d6fe34d7 100644
--- a/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf b/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf
index 84704812..f4d15a6c 100644
--- a/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf
+++ b/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Bluetooth Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf b/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf
index 7c75b522..36cb2f08 100644
--- a/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Android Accessory Mode Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf b/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf
index af07c395..f3ed928f 100644
--- a/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf b/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf
index 8255519a..237d312e 100644
--- a/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf b/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
index d9685efd..ae6cafac 100644
--- a/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Generic HID Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf
index c7c037a8..575abd0e 100644
--- a/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf b/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
index 2557f330..e626e69b 100644
--- a/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
index 00a850d3..72a0fb75 100644
--- a/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MIDIHost/Doxygen.conf b/Demos/Host/LowLevel/MIDIHost/Doxygen.conf
index 321cffdd..1d898aca 100644
--- a/Demos/Host/LowLevel/MIDIHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MIDIHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf b/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
index 2522f53f..086bf674 100644
--- a/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MouseHost/Doxygen.conf b/Demos/Host/LowLevel/MouseHost/Doxygen.conf
index 618c4d84..29459d8b 100644
--- a/Demos/Host/LowLevel/MouseHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MouseHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
index b2370b96..35b3dd06 100644
--- a/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo (Using HID Descriptor P
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/PrinterHost/Doxygen.conf b/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
index 791fe729..af83229f 100644
--- a/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Printer Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf b/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf
index 78a37f24..dac7bf3c 100644
--- a/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/StillImageHost/Doxygen.conf b/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
index 6341892c..f9ebf151 100644
--- a/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Still Image Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf b/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf
index 852d288b..d6fe34d7 100644
--- a/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/LUFA/Doxygen.conf b/LUFA/Doxygen.conf
index 0edee54c..5c3bf65b 100644
--- a/LUFA/Doxygen.conf
+++ b/LUFA/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 15
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = YES
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1727,7 +1721,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/LUFA/DoxygenPages/SoftwareBootloaderJump.txt b/LUFA/DoxygenPages/SoftwareBootloaderJump.txt
index 1fad85fb..09de9234 100644
--- a/LUFA/DoxygenPages/SoftwareBootloaderJump.txt
+++ b/LUFA/DoxygenPages/SoftwareBootloaderJump.txt
@@ -25,15 +25,15 @@
  *  #include <avr/wdt.h>
  *  #include <avr/io.h>
  *  #include <util/delay.h>
- *
+ *  
  *  #include <LUFA/Common/Common.h>
  *  #include <LUFA/Drivers/USB/USB.h>
- *
+ *  
  *  uint32_t Boot_Key ATTR_NO_INIT;
- *
+ *  
  *  #define MAGIC_BOOT_KEY            0xDC42ACCA
  *  #define BOOTLOADER_START_ADDRESS  (FLASH_SIZE_BYTES - BOOTLOADER_SEC_SIZE_BYTES)
- *
+ *  
  *  void Bootloader_Jump_Check(void) ATTR_INIT_SECTION(3);
  *  void Bootloader_Jump_Check(void)
  *  {
@@ -44,18 +44,18 @@
  *          ((void (*)(void))BOOTLOADER_START_ADDRESS)();
  *      }
  *  }
- *
+ *  
  *  void Jump_To_Bootloader(void)
  *  {
  *      // If USB is used, detach from the bus and reset it
  *      USB_Disable();
- *
+ *      
  *      // Disable all interrupts
  *      cli();
- *
+ *      
  *      // Wait two seconds for the USB detachment to register on the host
  *      Delay_MS(2000);
- *
+ *      
  *      // Set the bootloader key to the magic value and force a reset
  *      Boot_Key = MAGIC_BOOT_KEY;
  *      wdt_enable(WDTO_250MS);
diff --git a/LUFA/DoxygenPages/Style/Footer.htm b/LUFA/DoxygenPages/Style/Footer.htm
index 70bce531..a72c5bdd 100644
--- a/LUFA/DoxygenPages/Style/Footer.htm
+++ b/LUFA/DoxygenPages/Style/Footer.htm
@@ -1,15 +1,35 @@
 <!--BEGIN GENERATE_TREEVIEW-->
-			<span style="margin-right: 20px; float: right;">
+	<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+		<ul>
+			<li class="footer" style="float:left !important;">
+				$generatedby
+				<a href="http://www.doxygen.org/index.html">
+					<img class="footer" src="$relpath$doxygen.png" alt="doxygen"/>
+				</a>
+				$doxygenversion
+			</li>
+
+			<li class="footer">
 				<a href="http://www.lufa-lib.org" title="LUFA Project Page">LUFA Project Page</a> | <a href="http://www.lufa-lib.org/support" title="LUFA Support List">Support Mailing List</a> | <a href="http://www.lufa-lib.org/donate" title="Donate to Support LUFA">Donate</a> | <a href="http://www.fourwalledcubicle.com" title="Four Walled Cubicle Website">Four Walled Cubicle</a> - LUFA, the Lightweight USB Framework for AVRs
-			</span>
+			</li>
 		</ul>
 	</div>
 <!--END GENERATE_TREEVIEW-->
 <!--BEGIN !GENERATE_TREEVIEW-->
 		<hr class="footer"/>
-		<span style="margin-right: 20px; float: right;">
-			<a href="http://www.lufa-lib.org" title="LUFA Project Page">LUFA Project Page</a> | <a href="http://www.lufa-lib.org/support" title="LUFA Support List">Support Mailing List</a> | <a href="http://www.lufa-lib.org/donate" title="Donate to Support LUFA">Donate</a> | <a href="http://www.fourwalledcubicle.com" title="Four Walled Cubicle Website">Four Walled Cubicle</a> - LUFA, the Lightweight USB Framework for AVRs
-		</span>
+		<div class="footer">
+			<span style="float: left;">
+				$generatedby
+				<a href="http://www.doxygen.org/index.html">
+					<img class="footer" src="$relpath$doxygen.png" alt="doxygen"/>
+				</a>
+				$doxygenversion
+			</span>
+
+			<span style="margin-right: 20px; float: right;">
+				<a href="http://www.lufa-lib.org" title="LUFA Project Page">LUFA Project Page</a> | <a href="http://www.lufa-lib.org/support" title="LUFA Support List">Support Mailing List</a> | <a href="http://www.lufa-lib.org/donate" title="Donate to Support LUFA">Donate</a> | <a href="http://www.fourwalledcubicle.com" title="Four Walled Cubicle Website">Four Walled Cubicle</a> - LUFA, the Lightweight USB Framework for AVRs
+			</span>
+		</div>
 <!--END !GENERATE_TREEVIEW-->
 	</body>
 </html>
\ No newline at end of file
diff --git a/LUFA/DoxygenPages/Style/Style.css b/LUFA/DoxygenPages/Style/Style.css
index 3bff51e7..b64f9de8 100644
--- a/LUFA/DoxygenPages/Style/Style.css
+++ b/LUFA/DoxygenPages/Style/Style.css
@@ -43,14 +43,11 @@
 		overflow:inherit;

 		width:auto !important;

 	}

-

-	pre.fragment

+	

+	.fragment

 	{

-		overflow:visible;

-		text-wrap:unrestricted;

-		white-space:pre-wrap;

-		word-wrap:break-word;

-	}

+		background-color: #FFFFFF !important;

+	}	

 }

 

 body,table,div,p,dl

@@ -81,9 +78,8 @@ div.contents table.memberdecls,.paramname
 

 h1

 {

-	font-size:30px;

+	font-size:25px;

 	margin-bottom:10px;

-	padding:0 0 20px;

 }

 

 h2

@@ -228,22 +224,55 @@ dl.el
 	margin-left:-1cm;

 }

 

-.fragment

-{

-	font-family:monospace, fixed;

-	font-size:105%;

+pre.fragment {

+        border: 1px solid #C4CFE5;

+        background-color: #FBFCFD;

+        padding: 4px 6px;

+        margin: 4px 8px 4px 2px;

+        overflow: auto;

+        word-wrap: break-word;

+        font-size:  9pt;

+        line-height: 125%;

+        font-family: monospace, fixed;

+        font-size: 105%;

 }

 

-pre.fragment

-{

-	background-color:#F8F8F8;

-	border:1px solid #C1CEE8;

-	font-size:10pt;

-	line-height:125%;

-	margin:4px 8px 4px 20px;

-	overflow:auto;

-	padding:4px 6px;

-	word-wrap:break-word;

+div.fragment {

+	padding: 4px;

+	margin: 4px;

+	background-color: #FBFCFD;

+	border: 1px solid #C4CFE5;

+}

+

+div.line {

+	font-family: monospace, fixed;

+	font-size: 13px;

+	line-height: 1.0;

+	text-wrap: unrestricted;

+	white-space: -moz-pre-wrap; /* Moz */

+	white-space: -pre-wrap;     /* Opera 4-6 */

+	white-space: -o-pre-wrap;   /* Opera 7 */

+	white-space: pre-wrap;      /* CSS3  */

+	word-wrap: break-word;      /* IE 5.5+ */

+	text-indent: -53px;

+	padding-left: 53px;

+	padding-bottom: 0px;

+	margin: 0px;

+}

+

+span.lineno {

+	padding-right: 4px;

+	text-align: right;

+	border-right: 2px solid #0F0;

+	background-color: #E8E8E8;

+	white-space: pre;

+}

+span.lineno a {

+	background-color: #D8D8D8;

+}

+

+span.lineno a:hover {

+	background-color: #C8C8C8;

 }

 

 div.ah

@@ -1090,4 +1119,4 @@ div.toc li.level3
 div.toc li.level4

 {

 	margin-left:45px;

-}
\ No newline at end of file
+}

diff --git a/LUFA/Drivers/Board/Buttons.h b/LUFA/Drivers/Board/Buttons.h
index c3d6c0d0..1b70a6bd 100644
--- a/LUFA/Drivers/Board/Buttons.h
+++ b/LUFA/Drivers/Board/Buttons.h
@@ -68,13 +68,13 @@
  *  \code
  *      // Initialize the button driver before first use
  *      Buttons_Init();
- *
+ *      
  *      printf("Waiting for button press...\r\n");
- *
+ *      
  *      // Loop until a board button has been pressed
  *      uint8_t ButtonPress;
  *      while (!(ButtonPress = Buttons_GetStatus())) {};
- *
+ *      
  *      // Display which button was pressed (assuming two board buttons)
  *      printf("Button pressed: %s\r\n", (ButtonPress == BUTTONS_BUTTON1) ? "Button 1" : "Button 2");
  *  \endcode
diff --git a/LUFA/Drivers/Board/Dataflash.h b/LUFA/Drivers/Board/Dataflash.h
index a5ae29dc..c9f66054 100644
--- a/LUFA/Drivers/Board/Dataflash.h
+++ b/LUFA/Drivers/Board/Dataflash.h
@@ -70,44 +70,44 @@
  *      SPI_Init(SPI_SPEED_FCPU_DIV_2 | SPI_ORDER_MSB_FIRST | SPI_SCK_LEAD_FALLING |
  *               SPI_SAMPLE_TRAILING | SPI_MODE_MASTER);
  *      Dataflash_Init();
- *
+ *      
  *      uint8_t WriteBuffer[DATAFLASH_PAGE_SIZE];
  *      uint8_t ReadBuffer[DATAFLASH_PAGE_SIZE];
- *
+ *      
  *      // Fill page write buffer with a repeating pattern
  *      for (uint16_t i = 0; i < DATAFLASH_PAGE_SIZE; i++)
  *        WriteBuffer[i] = (i & 0xFF);
- *
+ *      
  *      // Must select the chip of interest first before operating on it
  *      Dataflash_SelectChip(DATAFLASH_CHIP1);
- *
+ *      
  *      // Write to the Dataflash's first internal memory buffer
  *      printf("Writing data to first dataflash buffer:\r\n");
  *      Dataflash_SendByte(DF_CMD_BUFF1WRITE);
  *      Dataflash_SendAddressBytes(0, 0);
- *
+ *      
  *      for (uint16_t i = 0; i < DATAFLASH_PAGE_SIZE; i++)
  *        Dataflash_SendByte(WriteBuffer[i]);
- *
+ *      
  *      // Commit the Dataflash's first memory buffer to the non-volatile FLASH memory
  *      printf("Committing page to non-volatile memory page index 5:\r\n");
  *      Dataflash_SendByte(DF_CMD_BUFF1TOMAINMEMWITHERASE);
  *      Dataflash_SendAddressBytes(5, 0);
  *      Dataflash_WaitWhileBusy();
- *
+ *      
  *      // Read the page from non-volatile FLASH memory into the Dataflash's second memory buffer
  *      printf("Reading data into second dataflash buffer:\r\n");
  *      Dataflash_SendByte(DF_CMD_MAINMEMTOBUFF2);
  *      Dataflash_SendAddressBytes(5, 0);
  *      Dataflash_WaitWhileBusy();
- *
+ *      
  *      // Read the Dataflash's second internal memory buffer
  *      Dataflash_SendByte(DF_CMD_BUFF2READ);
  *      Dataflash_SendAddressBytes(0, 0);
- *
+ *      
  *      for (uint16_t i = 0; i < DATAFLASH_PAGE_SIZE; i++)
  *        ReadBuffer[i] = Dataflash_ReceiveByte();
- *
+ *      
  *      // Deselect the chip after use
  *      Dataflash_DeselectChip();
  *  \endcode
diff --git a/LUFA/Drivers/Board/Joystick.h b/LUFA/Drivers/Board/Joystick.h
index 0a1f9fa7..63d28e83 100644
--- a/LUFA/Drivers/Board/Joystick.h
+++ b/LUFA/Drivers/Board/Joystick.h
@@ -67,22 +67,22 @@
  *  \code
  *      // Initialize the board Joystick driver before first use
  *      Joystick_Init();
- *
+ *      
  *      printf("Waiting for joystick movement...\r\n");
- *
+ *      
  *      // Loop until a the joystick has been moved
  *      uint8_t JoystickMovement;
  *      while (!(JoystickMovement = Joystick_GetStatus())) {};
- *
+ *      
  *      // Display which direction the joystick was moved in
  *      printf("Joystick moved:\r\n");
- *
+ *      
  *      if (JoystickMovement & (JOY_UP | JOY_DOWN))
  *        printf("%s ", (JoystickMovement & JOY_UP) ? "Up" : "Down");
- *
+ *      
  *      if (JoystickMovement & (JOY_LEFT | JOY_RIGHT))
  *        printf("%s ", (JoystickMovement & JOY_LEFT) ? "Left" : "Right");
- *
+ *      
  *      if (JoystickMovement & JOY_PRESS)
  *        printf("Pressed");
  *  \endcode
diff --git a/LUFA/Drivers/Board/LEDs.h b/LUFA/Drivers/Board/LEDs.h
index f6f9d82f..97cb81a5 100644
--- a/LUFA/Drivers/Board/LEDs.h
+++ b/LUFA/Drivers/Board/LEDs.h
@@ -76,7 +76,7 @@
  *  \code
  *      // Initialize the board LED driver before first use
  *      LEDs_Init();
- *
+ *      
  *      // Turn on each of the four LEDs in turn
  *      LEDs_SetAllLEDs(LEDS_LED1);
  *      Delay_MS(500);
@@ -86,11 +86,11 @@
  *      Delay_MS(500);
  *      LEDs_SetAllLEDs(LEDS_LED4);
  *      Delay_MS(500);
- *
+ *      
  *      // Turn on all LEDs
  *      LEDs_SetAllLEDs(LEDS_ALL_LEDS);
  *      Delay_MS(1000);
- *
+ *      
  *      // Turn on LED 1, turn off LED 2, leaving LEDs 3 and 4 in their current state
  *      LEDs_ChangeLEDs((LEDS_LED1 | LEDS_LED2), LEDS_LED1);
  *  \endcode
diff --git a/LUFA/Drivers/Board/Temperature.h b/LUFA/Drivers/Board/Temperature.h
index ef967967..54ca957a 100644
--- a/LUFA/Drivers/Board/Temperature.h
+++ b/LUFA/Drivers/Board/Temperature.h
@@ -56,7 +56,7 @@
  *      // Initialize the ADC and board temperature sensor drivers before first use
  *      ADC_Init(ADC_FREE_RUNNING | ADC_PRESCALE_128);
  *      Temperature_Init();
- *
+ *      
  *      // Display converted temperature in degrees Celsius
  *      printf("Current Temperature: %d Degrees\r\n", Temperature_GetTemperature());
  *  \endcode
diff --git a/LUFA/Drivers/Misc/RingBuffer.h b/LUFA/Drivers/Misc/RingBuffer.h
index df7e7021..b0bc5c55 100644
--- a/LUFA/Drivers/Misc/RingBuffer.h
+++ b/LUFA/Drivers/Misc/RingBuffer.h
@@ -65,23 +65,23 @@
  *      // Create the buffer structure and its underlying storage array
  *      RingBuffer_t Buffer;
  *      uint8_t      BufferData[128];
- *
+ *      
  *      // Initialize the buffer with the created storage array
  *      RingBuffer_InitBuffer(&Buffer, BufferData, sizeof(BufferData));
- *
+ *      
  *      // Insert some data into the buffer
  *      RingBuffer_Insert(Buffer, 'H');
  *      RingBuffer_Insert(Buffer, 'E');
  *      RingBuffer_Insert(Buffer, 'L');
  *      RingBuffer_Insert(Buffer, 'L');
  *      RingBuffer_Insert(Buffer, 'O');
- *
+ *      
  *      // Cache the number of stored bytes in the buffer
  *      uint16_t BufferCount = RingBuffer_GetCount(&Buffer);
- *
+ *      
  *      // Printer stored data length
  *      printf("Buffer Length: %d, Buffer Data: \r\n", BufferCount);
- *
+ *      
  *      // Print contents of the buffer one character at a time
  *      while (BufferCount--)
  *        putc(RingBuffer_Remove(&Buffer));
diff --git a/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h
index ec80dd24..c04d2ba8 100644
--- a/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h
@@ -55,14 +55,14 @@
  *  \code
  *      // Initialize the ADC driver before first use
  *      ADC_Init(ADC_FREE_RUNNING | ADC_PRESCALE_32);
- *
+ *      
  *      // Must setup the ADC channel to read beforehand
  *      ADC_SetupChannel(1);
- *
+ *      
  *      // Perform a single conversion of the ADC channel 1
  *      ADC_GetChannelReading(ADC_REFERENCE_AVCC | ADC_RIGHT_ADJUSTED | ADC_CHANNEL1);
  *      printf("Conversion Result: %d\r\n", ADC_GetResult());
- *
+ *      
  *      // Start reading ADC channel 1 in free running (continuous conversion) mode
  *      ADC_StartReading(ADC_REFERENCE_AVCC | ADC_RIGHT_ADJUSTED | ADC_CHANNEL1);
  *      for (;;)
diff --git a/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h
index 2e396ed5..3ca03760 100644
--- a/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h
@@ -56,17 +56,17 @@
  *      // Initialize the SPI driver before first use
  *      SPI_Init(SPI_SPEED_FCPU_DIV_2 | SPI_ORDER_MSB_FIRST | SPI_SCK_LEAD_FALLING |
  *               SPI_SAMPLE_TRAILING | SPI_MODE_MASTER);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SPI_SendByte(0x01);
  *      SPI_SendByte(0x02);
  *      SPI_SendByte(0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SPI_ReceiveByte();
  *      uint8_t Byte2 = SPI_ReceiveByte();
  *      uint8_t Byte3 = SPI_ReceiveByte();
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SPI_TransferByte(0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h
index 562aaecf..24d341f0 100644
--- a/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h
@@ -53,17 +53,17 @@
  *  \code
  *      // Initialize the Master SPI mode USART driver before first use, with 1Mbit baud
  *      SerialSPI_Init((USART_SPI_SCK_LEAD_RISING | SPI_SAMPLE_LEADING | SPI_ORDER_MSB_FIRST), 1000000);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SerialSPI_SendByte(0x01);
  *      SerialSPI_SendByte(0x02);
  *      SerialSPI_SendByte(0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SerialSPI_ReceiveByte();
  *      uint8_t Byte2 = SerialSPI_ReceiveByte();
  *      uint8_t Byte3 = SerialSPI_ReceiveByte();
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SerialSPI_TransferByte(0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h
index 687ea74a..b7b50f43 100644
--- a/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h
@@ -53,10 +53,10 @@
  *  \code
  *      // Initialize the serial USART driver before first use, with 9600 baud (and no double-speed mode)
  *      Serial_Init(9600, false);
- *
+ *      
  *      // Send a string through the USART
  *      Serial_TxString("Test String\r\n");
- *
+ *      
  *      // Receive a byte through the USART
  *      uint8_t DataByte = Serial_RxByte();
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h
index b9131df3..38ad1f3e 100644
--- a/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h
@@ -54,35 +54,35 @@
  *  \code
  *      // Initialize the TWI driver before first use at 200KHz
  *      TWI_Init(TWI_BIT_PRESCALE_1, TWI_BITLENGTH_FROM_FREQ(1, 200000));
- *
+ *      
  *      // Start a write session to device at device address 0xA0, internal address 0xDC with a 10ms timeout
  *      if (TWI_StartTransmission(0xA0 | TWI_ADDRESS_WRITE, 10) == TWI_ERROR_NoError)
  *      {
  *          TWI_SendByte(0xDC);
- *
+ *          
  *          TWI_SendByte(0x01);
  *          TWI_SendByte(0x02);
  *          TWI_SendByte(0x03);
- *
+ *          
  *          // Must stop transmission afterwards to release the bus
  *          TWI_StopTransmission();
  *      }
- *
+ *      
  *      // Start a read session to device at address 0xA0, internal address 0xDC with a 10ms timeout
  *      if (TWI_StartTransmission(0xA0 | TWI_ADDRESS_WRITE, 10) == TWI_ERROR_NoError)
  *      {
  *          TWI_SendByte(0xDC);
  *          TWI_StopTransmission();
- *
+ *          
  *          if (TWI_StartTransmission(0xA0 | TWI_ADDRESS_READ, 10) == TWI_ERROR_NoError)
  *          {
  *              uint8_t Byte1, Byte2, Byte3;
- *
+ *              
  *              // Read three bytes, acknowledge after the third byte is received
  *              TWI_ReceiveByte(&Byte1, false);
  *              TWI_ReceiveByte(&Byte2, false);
  *              TWI_ReceiveByte(&Byte3, true);
- *
+ *              
  *              // Must stop transmission afterwards to release the bus
  *              TWI_StopTransmission();
  *          }
@@ -93,18 +93,18 @@
  *  \code
  *      // Initialize the TWI driver before first use at 200KHz
  *      TWI_Init(TWI_BIT_PRESCALE_1, TWI_BITLENGTH_FROM_FREQ(1, 200000));
- *
+ *      
  *      // Start a write session to device at device address 0xA0, internal address 0xDC with a 10ms timeout
  *      uint8_t InternalWriteAddress = 0xDC;
  *      uint8_t WritePacket[3] = {0x01, 0x02, 0x03};
- *
+ *      
  *      TWI_WritePacket(0xA0, 10, &InternalWriteAddress, sizeof(InternalWriteAddress),
  *                      &WritePacket, sizeof(WritePacket);
- *
+ *      
  *      // Start a read session to device at address 0xA0, internal address 0xDC with a 10ms timeout
  *      uint8_t InternalReadAddress = 0xDC;
  *      uint8_t ReadPacket[3];
- *
+ *      
  *      TWI_ReadPacket(0xA0, 10, &InternalReadAddress, sizeof(InternalReadAddress),
  *                     &ReadPacket, sizeof(ReadPacket);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h b/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h
index a21ac1ca..8c57dacd 100644
--- a/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h
+++ b/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h
@@ -53,17 +53,17 @@
  *      SPI_Init(&SPIC,
  *               SPI_SPEED_FCPU_DIV_2 | SPI_ORDER_MSB_FIRST | SPI_SCK_LEAD_FALLING |
  *               SPI_SAMPLE_TRAILING | SPI_MODE_MASTER);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SPI_SendByte(&SPIC, 0x01);
  *      SPI_SendByte(&SPIC, 0x02);
  *      SPI_SendByte(&SPIC, 0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SPI_ReceiveByte(&SPIC);
  *      uint8_t Byte2 = SPI_ReceiveByte(&SPIC);
  *      uint8_t Byte3 = SPI_ReceiveByte(&SPIC);
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SPI_TransferByte(&SPIC, 0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h b/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h
index a0e9e337..64d57a3f 100644
--- a/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h
+++ b/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h
@@ -53,17 +53,17 @@
  *  \code
  *      // Initialize the Master SPI mode USART driver before first use, with 1Mbit baud
  *      SerialSPI_Init(&USARTD0, (USART_SPI_SCK_LEAD_RISING | USART_SPI_SAMPLE_LEADING | USART_SPI_ORDER_MSB_FIRST), 1000000);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SerialSPI_SendByte(&USARTD0, 0x01);
  *      SerialSPI_SendByte(&USARTD0, 0x02);
  *      SerialSPI_SendByte(&USARTD0, 0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SerialSPI_ReceiveByte(&USARTD);
  *      uint8_t Byte2 = SerialSPI_ReceiveByte(&USARTD);
  *      uint8_t Byte3 = SerialSPI_ReceiveByte(&USARTD);
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SerialSPI_TransferByte(&USARTD0, 0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h b/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h
index 283732f0..c2cb77fd 100644
--- a/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h
+++ b/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h
@@ -53,10 +53,10 @@
  *  \code
  *      // Initialize the serial USART driver before first use, with 9600 baud (and no double-speed mode)
  *      Serial_Init(&USARTD0, 9600, false);
- *
+ *      
  *      // Send a string through the USART
  *      Serial_TxString(&USARTD0, "Test String\r\n");
- *
+ *      
  *      // Receive a byte through the USART
  *      uint8_t DataByte = Serial_RxByte(&USARTD0);
  *  \endcode
diff --git a/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h b/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h
index ecc1fb0b..072d8593 100644
--- a/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h
+++ b/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h
@@ -87,7 +87,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Discard_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -98,13 +98,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Discard_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -140,7 +140,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Null_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -151,13 +151,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Null_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -199,7 +199,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                            NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

@@ -276,7 +276,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                           NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

@@ -289,14 +289,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                              &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

diff --git a/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h b/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h
index e9da4225..53316f2f 100644
--- a/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h
+++ b/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h
@@ -85,7 +85,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Discard_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -96,13 +96,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Discard_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -137,7 +137,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Null_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -148,13 +148,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Null_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -198,7 +198,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                        NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

@@ -211,14 +211,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                           &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -279,7 +279,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                       NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

@@ -292,14 +292,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                          &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

diff --git a/LUFA/Drivers/USB/Core/ConfigDescriptor.h b/LUFA/Drivers/USB/Core/ConfigDescriptor.h
index 5e97939e..22e76cba 100644
--- a/LUFA/Drivers/USB/Core/ConfigDescriptor.h
+++ b/LUFA/Drivers/USB/Core/ConfigDescriptor.h
@@ -76,7 +76,7 @@
 			 *  uint8_t* CurrDescriptor = &ConfigDescriptor[0]; // Pointing to the configuration header
 			 *  USB_Descriptor_Configuration_Header_t* ConfigHeaderPtr = DESCRIPTOR_PCAST(CurrDescriptor,
 			 *                                                           USB_Descriptor_Configuration_Header_t);
-			 *
+			 *  
 			 *  // Can now access elements of the configuration header struct using the -> indirection operator
 			 *  \endcode
 			 */
@@ -90,7 +90,7 @@
 			 *  uint8_t* CurrDescriptor = &ConfigDescriptor[0]; // Pointing to the configuration header
 			 *  USB_Descriptor_Configuration_Header_t ConfigHeader = DESCRIPTOR_CAST(CurrDescriptor,
 			 *                                                       USB_Descriptor_Configuration_Header_t);
-			 *
+			 *  
 			 *  // Can now access elements of the configuration header struct using the . operator
 			 *  \endcode
 			 */
@@ -231,7 +231,7 @@
 			 *  Usage Example:
 			 *  \code
 			 *  uint8_t EndpointSearcher(void* CurrentDescriptor); // Comparator Prototype
-			 *
+			 *  
 			 *  uint8_t EndpointSearcher(void* CurrentDescriptor)
 			 *  {
 			 *     if (DESCRIPTOR_TYPE(CurrentDescriptor) == DTYPE_Endpoint)
@@ -239,8 +239,9 @@
 			 *     else
 			 *         return DESCRIPTOR_SEARCH_NotFound;
 			 *  }
-			 *
+			 *  
 			 *  //...
+			 *  
 			 *  // After retrieving configuration descriptor:
 			 *  if (USB_Host_GetNextDescriptorComp(&BytesRemaining, &CurrentConfigLoc, EndpointSearcher) ==
 			 *      Descriptor_Search_Comp_Found)
diff --git a/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h b/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h
index 335e1978..40a54ee1 100644
--- a/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h
+++ b/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h
@@ -87,7 +87,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Discard_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -98,13 +98,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Discard_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -140,7 +140,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Null_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -151,13 +151,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Null_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -199,7 +199,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                            NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

@@ -212,14 +212,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                               &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -276,7 +276,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                           NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

@@ -289,14 +289,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                              &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

diff --git a/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h b/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h
index 3f211182..cb8a28c8 100644
--- a/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h
+++ b/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h
@@ -85,24 +85,24 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Discard_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

 			 *  }

 			 *  \endcode

-			 *

+			 *  

 			 *  <b>Partial Stream Transfers Example:</b>

 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Discard_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -137,7 +137,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Null_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -148,13 +148,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Null_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -198,7 +198,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                        NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

@@ -211,14 +211,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                           &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -279,7 +279,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                       NULL)) != PIPE_RWSTREAM_NoError)

 			 *  {

@@ -292,14 +292,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                          &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

diff --git a/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h b/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h
index 711d7a3a..3269d2b1 100644
--- a/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h
+++ b/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h
@@ -87,7 +87,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Discard_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -98,13 +98,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Discard_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -140,7 +140,7 @@
 			 *  <b>Single Stream Transfer Example:</b>

 			 *  \code

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Null_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *       // Stream failed to complete - check ErrorCode here

@@ -151,13 +151,13 @@
 			 *  \code

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Null_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -199,7 +199,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                            NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

@@ -212,14 +212,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                               &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

@@ -276,7 +276,7 @@
 			 *  \code

 			 *  uint8_t DataStream[512];

 			 *  uint8_t ErrorCode;

-			 *

+			 *  

 			 *  if ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                           NULL)) != ENDPOINT_RWSTREAM_NoError)

 			 *  {

@@ -289,14 +289,14 @@
 			 *  uint8_t  DataStream[512];

 			 *  uint8_t  ErrorCode;

 			 *  uint16_t BytesProcessed;

-			 *

+			 *  

 			 *  BytesProcessed = 0;

 			 *  while ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),

 			 *                                              &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)

 			 *  {

 			 *      // Stream not yet complete - do other actions here, abort if required

 			 *  }

-			 *

+			 *  

 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)

 			 *  {

 			 *      // Stream failed to complete - check ErrorCode here

diff --git a/LUFA/Drivers/USB/USB.h b/LUFA/Drivers/USB/USB.h
index c99c1d26..626635c8 100644
--- a/LUFA/Drivers/USB/USB.h
+++ b/LUFA/Drivers/USB/USB.h
@@ -189,7 +189,7 @@
  *  void EVENT_USB_Device_ConfigurationChanged(void)
  *  {
  *      LEDs_SetAllLEDs(LEDMASK_USB_READY);
- *
+ *      
  *      if (!(Audio_Device_ConfigureEndpoints(&My_Audio_Interface)))
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *  }
@@ -205,14 +205,14 @@
  *  int main(void)
  *  {
  *      SetupHardware();
- *
+ *      
  *      LEDs_SetAllLEDs(LEDMASK_USB_NOTREADY);
- *
+ *      
  *      for (;;)
  *      {
  *          if (USB_DeviceState != DEVICE_STATE_Configured)
  *            Create_And_Process_Samples();
- *
+ *          
  *          Audio_Device_USBTask(&My_Audio_Interface);
  *          USB_USBTask();
  *      }
@@ -293,30 +293,30 @@
  *  void EVENT_USB_Host_DeviceEnumerationComplete(void)
  *  {
  *      LEDs_SetAllLEDs(LEDMASK_USB_ENUMERATING);
- *  
+ *      
  *      uint16_t ConfigDescriptorSize;
  *      uint8_t  ConfigDescriptorData[512];
- *  
+ *      
  *      if (USB_Host_GetDeviceConfigDescriptor(1, &ConfigDescriptorSize, ConfigDescriptorData,
  *                                             sizeof(ConfigDescriptorData)) != HOST_GETCONFIG_Successful)
  *      {
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *          return;
  *      }
- *  
+ *      
  *      if (MIDI_Host_ConfigurePipes(&Keyboard_MIDI_Interface,
  *                                   ConfigDescriptorSize, ConfigDescriptorData) != MIDI_ENUMERROR_NoError)
  *      {
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *          return;
  *      }
- *  
+ *      
  *      if (USB_Host_SetDeviceConfiguration(1) != HOST_SENDCONTROL_Successful)
  *      {
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *          return;
  *      }
- *  
+ *      
  *      LEDs_SetAllLEDs(LEDMASK_USB_READY);
  *  }
  *  \endcode
@@ -342,14 +342,14 @@
  *  int main(void)
  *  {
  *      SetupHardware();
- *
+ *      
  *      LEDs_SetAllLEDs(LEDMASK_USB_NOTREADY);
- *
+ *      
  *      for (;;)
  *      {
  *          if (USB_HostState != HOST_STATE_Configured)
  *              Create_And_Process_Samples();
- *
+ *          
  *          MIDI_Host_USBTask(&My_Audio_Interface);
  *          USB_USBTask();
  *      }
diff --git a/LUFA/Platform/UC3/ClockManagement.h b/LUFA/Platform/UC3/ClockManagement.h
index d0d8f71e..2cd96d2e 100644
--- a/LUFA/Platform/UC3/ClockManagement.h
+++ b/LUFA/Platform/UC3/ClockManagement.h
@@ -50,16 +50,16 @@
  *  Usage Example:
  *  \code
  *		#include <LUFA/Platform/UC3/ClockManagement.h>
- *
+ *      
  *		void main(void)
  *		{
  *			// Start the master external oscillator which will be used as the main clock reference
  *			AVR32CLK_StartExternalOscillator(0, EXOSC_MODE_8MHZ_OR_MORE, EXOSC_START_0CLK);
- *
+ *          
  *			// Start the PLL for the CPU clock, switch CPU to it
  *			AVR32CLK_StartPLL(0, CLOCK_SRC_OSC0, 12000000, F_CPU);
  *			AVR32CLK_SetCPUClockSource(CLOCK_SRC_PLL0, F_CPU);
- *
+ *          
  *			// Start the PLL for the USB Generic Clock module
  *			AVR32CLK_StartPLL(1, CLOCK_SRC_OSC0, 12000000, 48000000);
  *		}
diff --git a/LUFA/Platform/UC3/InterruptManagement.h b/LUFA/Platform/UC3/InterruptManagement.h
index 8dd1dc3d..af99f087 100644
--- a/LUFA/Platform/UC3/InterruptManagement.h
+++ b/LUFA/Platform/UC3/InterruptManagement.h
@@ -51,12 +51,12 @@
  *  Usage Example:
  *  \code
  *		#include <LUFA/Platform/UC3/InterruptManagement.h>
- *
+ *      
  *		ISR(USB_Group_IRQ_Handler)
  *		{
  *			// USB group handler code here
  *		}
- *
+ *      
  *		void main(void)
  *		{
  *			INTC_Init();
diff --git a/LUFA/Platform/XMEGA/ClockManagement.h b/LUFA/Platform/XMEGA/ClockManagement.h
index 9b3b5624..feef8898 100644
--- a/LUFA/Platform/XMEGA/ClockManagement.h
+++ b/LUFA/Platform/XMEGA/ClockManagement.h
@@ -50,13 +50,13 @@
  *  Usage Example:
  *  \code
  *   	#include <LUFA/Platform/XMEGA/ClockManagement.h>
- *
+ *      
  *   	void main(void)
  *   	{
  *   		// Start the PLL to multiply the 2MHz RC oscillator to F_CPU and switch the CPU core to run from it
  *   		XMEGACLK_StartPLL(CLOCK_SRC_INT_RC2MHZ, 2000000, F_CPU);
  *   		XMEGACLK_SetCPUClockSource(CLOCK_SRC_PLL);
- *
+ *          
  *   		// Start the 32MHz internal RC oscillator and start the DFLL to increase it to F_USB using the USB SOF as a reference
  *   		XMEGACLK_StartInternalOscillator(CLOCK_SRC_INT_RC32MHZ);
  *   		XMEGACLK_StartDFLL(CLOCK_SRC_INT_RC32MHZ, DFLL_REF_INT_USBSOF, F_USB);
diff --git a/Projects/AVRISP-MKII/Doxygen.conf b/Projects/AVRISP-MKII/Doxygen.conf
index 12a6b9c7..24e139ab 100644
--- a/Projects/AVRISP-MKII/Doxygen.conf
+++ b/Projects/AVRISP-MKII/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "AVRISP-MKII Clone Programmer Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/Benito/Doxygen.conf b/Projects/Benito/Doxygen.conf
index 44ff2a40..64e72a1a 100644
--- a/Projects/Benito/Doxygen.conf
+++ b/Projects/Benito/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Benito Arduino Programmer Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/HIDReportViewer/Doxygen.conf b/Projects/HIDReportViewer/Doxygen.conf
index b792c67b..4906ca5e 100644
--- a/Projects/HIDReportViewer/Doxygen.conf
+++ b/Projects/HIDReportViewer/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "HID Device Report Viewer Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/LEDNotifier/Doxygen.conf b/Projects/LEDNotifier/Doxygen.conf
index 562fcd8a..61467471 100644
--- a/Projects/LEDNotifier/Doxygen.conf
+++ b/Projects/LEDNotifier/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - USB LED Notifier Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -963,12 +957,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -977,6 +965,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1134,7 +1133,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1155,11 +1154,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1728,7 +1722,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/MIDIToneGenerator/Doxygen.conf b/Projects/MIDIToneGenerator/Doxygen.conf
index 50223a88..277c6159 100644
--- a/Projects/MIDIToneGenerator/Doxygen.conf
+++ b/Projects/MIDIToneGenerator/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Tone Generator Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/Magstripe/Doxygen.conf b/Projects/Magstripe/Doxygen.conf
index 5bde2d85..aaddc869 100644
--- a/Projects/Magstripe/Doxygen.conf
+++ b/Projects/Magstripe/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Denver Gingerich's Stripe Snoop Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/MediaController/Doxygen.conf b/Projects/MediaController/Doxygen.conf
index 4ef61870..32c532d9 100644
--- a/Projects/MediaController/Doxygen.conf
+++ b/Projects/MediaController/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Media Controller Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/MissileLauncher/Doxygen.conf b/Projects/MissileLauncher/Doxygen.conf
index 48083287..512649df 100644
--- a/Projects/MissileLauncher/Doxygen.conf
+++ b/Projects/MissileLauncher/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Dave Fletcher's Missile Launcher Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/RelayBoard/Doxygen.conf b/Projects/RelayBoard/Doxygen.conf
index 03778cb8..dc116f0c 100644
--- a/Projects/RelayBoard/Doxygen.conf
+++ b/Projects/RelayBoard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "OB's Dual-Relay Outlet Control Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/SerialToLCD/Doxygen.conf b/Projects/SerialToLCD/Doxygen.conf
index eaa8e168..b16a3b8a 100644
--- a/Projects/SerialToLCD/Doxygen.conf
+++ b/Projects/SerialToLCD/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Simon Foster's USB Serial to HD44780 LCD Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/TempDataLogger/Doxygen.conf b/Projects/TempDataLogger/Doxygen.conf
index 7a383219..70f6e0ae 100644
--- a/Projects/TempDataLogger/Doxygen.conf
+++ b/Projects/TempDataLogger/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Temperature Datalogger Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -961,12 +955,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -975,6 +963,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1132,7 +1131,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1153,11 +1152,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/USBtoSerial/Doxygen.conf b/Projects/USBtoSerial/Doxygen.conf
index 57f8a9a6..ae0ed482 100644
--- a/Projects/USBtoSerial/Doxygen.conf
+++ b/Projects/USBtoSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - USB to Serial Device Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/Webserver/Doxygen.conf b/Projects/Webserver/Doxygen.conf
index 691ce6a7..3d431fd0 100644
--- a/Projects/Webserver/Doxygen.conf
+++ b/Projects/Webserver/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - uIP Powered Webserver Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -961,12 +955,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -975,6 +963,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1132,7 +1131,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1153,11 +1152,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/XPLAINBridge/Doxygen.conf b/Projects/XPLAINBridge/Doxygen.conf
index 2e5c3a3c..827d892c 100644
--- a/Projects/XPLAINBridge/Doxygen.conf
+++ b/Projects/XPLAINBridge/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - XPLAIN Serial Bridge/PDI Programmer Pro
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.