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.

16 files changed, 240 insertions, 336 deletions

diff --git a/Demos/Device/ClassDriver/AudioInput/Doxygen.conf b/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
index 3d3345971..d217aa443 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 392086e96..4cd9e9c5b 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 3c9c10e2f..0f78680c3 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 78e4ff04a..7b71c2054 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 348faaf11..407d08a86 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 57095df3d..0b47b1a32 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 4016a2e42..a7357cb18 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 b0ed4dc40..c3696bbd9 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 d17ed60c7..f95325f80 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 9da2792a0..4ef067503 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 cf8be4ea5..4f8b9e59d 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 d92f7f637..1dd2ccd02 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 1da1f868b..da74f6b48 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 2cd6e221e..ebe72a5d9 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 c507f2691..c38f51df6 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 6aaf97067..fea97b2d9 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.