diff --git a/Bootloaders/CDC/Doxygen.conf b/Bootloaders/CDC/Doxygen.conf
index b9738b12415..4ef22ea2a7b 100644
--- a/Bootloaders/CDC/Doxygen.conf
+++ b/Bootloaders/CDC/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Bootloaders/DFU/Doxygen.conf b/Bootloaders/DFU/Doxygen.conf
index b4c4bbc3941..5b3ab93668b 100644
--- a/Bootloaders/DFU/Doxygen.conf
+++ b/Bootloaders/DFU/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/AudioInput/Doxygen.conf b/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
index a247f5677e1..9fca380be03 100644
--- a/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
+++ b/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf b/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
index 2a2567e8241..6539c2b8b8d 100644
--- a/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
+++ b/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/CDC/Doxygen.conf b/Demos/Device/ClassDriver/CDC/Doxygen.conf
index ba8038fce8c..fa91d220753 100644
--- a/Demos/Device/ClassDriver/CDC/Doxygen.conf
+++ b/Demos/Device/ClassDriver/CDC/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/DualCDC/Doxygen.conf b/Demos/Device/ClassDriver/DualCDC/Doxygen.conf
index 5bd04f3deaf..04af23b64c6 100644
--- a/Demos/Device/ClassDriver/DualCDC/Doxygen.conf
+++ b/Demos/Device/ClassDriver/DualCDC/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/GenericHID/Doxygen.conf b/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
index 3f37a4603aa..c2a65fc8fcc 100644
--- a/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
+++ b/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/Joystick/Doxygen.conf b/Demos/Device/ClassDriver/Joystick/Doxygen.conf
index 01bcef99a6c..f1f595aac93 100644
--- a/Demos/Device/ClassDriver/Joystick/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Joystick/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/Keyboard/Doxygen.conf b/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
index ae9ed8b2704..b600c3e4750 100644
--- a/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf b/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
index 2f21cdba787..d8edaebd7ac 100644
--- a/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/MIDI/Doxygen.conf b/Demos/Device/ClassDriver/MIDI/Doxygen.conf
index 4091d0b20d2..3a1e3ec6b63 100644
--- a/Demos/Device/ClassDriver/MIDI/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MIDI/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/MassStorage/Doxygen.conf b/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
index fa7b084c9e2..04475c4eae4 100644
--- a/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/MassStorage/Lib/DataflashManager.c b/Demos/Device/ClassDriver/MassStorage/Lib/DataflashManager.c
index f335b679824..1c584e71c3b 100644
--- a/Demos/Device/ClassDriver/MassStorage/Lib/DataflashManager.c
+++ b/Demos/Device/ClassDriver/MassStorage/Lib/DataflashManager.c
@@ -43,6 +43,7 @@
  *  the pre-selected data OUT endpoint. This routine reads in OS sized blocks from the endpoint and writes
  *  them to the dataflash in Dataflash page sized blocks.
  *
+ *  \param[in] MSInterfaceInfo  Pointer to a structure containing a Mass Storage Class configuration and state.
  *  \param[in] BlockAddress  Data block starting address for the write sequence
  *  \param[in] TotalBlocks   Number of blocks of data to write
  */
@@ -174,6 +175,7 @@ void DataflashManager_WriteBlocks(USB_ClassInfo_MS_Device_t* MSInterfaceInfo, co
  *  the pre-selected data IN endpoint. This routine reads in Dataflash page sized blocks from the Dataflash
  *  and writes them in OS sized blocks to the endpoint.
  *
+ *  \param[in] MSInterfaceInfo  Pointer to a structure containing a Mass Storage Class configuration and state.
  *  \param[in] BlockAddress  Data block starting address for the read sequence
  *  \param[in] TotalBlocks   Number of blocks of data to read
  */
diff --git a/Demos/Device/ClassDriver/Mouse/Doxygen.conf b/Demos/Device/ClassDriver/Mouse/Doxygen.conf
index 9e8e15ec59d..704e17d79ac 100644
--- a/Demos/Device/ClassDriver/Mouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Mouse/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf b/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
index d76cbe07266..48a04723b20 100644
--- a/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
+++ b/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/ClassDriver/USBtoSerial/Doxygen.conf b/Demos/Device/ClassDriver/USBtoSerial/Doxygen.conf
index 7564c95bf60..ceb4e6ad0dc 100644
--- a/Demos/Device/ClassDriver/USBtoSerial/Doxygen.conf
+++ b/Demos/Device/ClassDriver/USBtoSerial/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/AudioInput/Doxygen.conf b/Demos/Device/LowLevel/AudioInput/Doxygen.conf
index a247f5677e1..9fca380be03 100644
--- a/Demos/Device/LowLevel/AudioInput/Doxygen.conf
+++ b/Demos/Device/LowLevel/AudioInput/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/AudioOutput/Doxygen.conf b/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
index 2a2567e8241..6539c2b8b8d 100644
--- a/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
+++ b/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/CDC/Doxygen.conf b/Demos/Device/LowLevel/CDC/Doxygen.conf
index ba8038fce8c..fa91d220753 100644
--- a/Demos/Device/LowLevel/CDC/Doxygen.conf
+++ b/Demos/Device/LowLevel/CDC/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/DualCDC/Doxygen.conf b/Demos/Device/LowLevel/DualCDC/Doxygen.conf
index 5bd04f3deaf..04af23b64c6 100644
--- a/Demos/Device/LowLevel/DualCDC/Doxygen.conf
+++ b/Demos/Device/LowLevel/DualCDC/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/GenericHID/Doxygen.conf b/Demos/Device/LowLevel/GenericHID/Doxygen.conf
index 3f37a4603aa..c2a65fc8fcc 100644
--- a/Demos/Device/LowLevel/GenericHID/Doxygen.conf
+++ b/Demos/Device/LowLevel/GenericHID/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/Joystick/Doxygen.conf b/Demos/Device/LowLevel/Joystick/Doxygen.conf
index 01bcef99a6c..f1f595aac93 100644
--- a/Demos/Device/LowLevel/Joystick/Doxygen.conf
+++ b/Demos/Device/LowLevel/Joystick/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/Keyboard/Doxygen.conf b/Demos/Device/LowLevel/Keyboard/Doxygen.conf
index ae9ed8b2704..b600c3e4750 100644
--- a/Demos/Device/LowLevel/Keyboard/Doxygen.conf
+++ b/Demos/Device/LowLevel/Keyboard/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf b/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
index 2f21cdba787..d8edaebd7ac 100644
--- a/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
+++ b/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/MIDI/Doxygen.conf b/Demos/Device/LowLevel/MIDI/Doxygen.conf
index 4091d0b20d2..3a1e3ec6b63 100644
--- a/Demos/Device/LowLevel/MIDI/Doxygen.conf
+++ b/Demos/Device/LowLevel/MIDI/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/MassStorage/Doxygen.conf b/Demos/Device/LowLevel/MassStorage/Doxygen.conf
index fa7b084c9e2..04475c4eae4 100644
--- a/Demos/Device/LowLevel/MassStorage/Doxygen.conf
+++ b/Demos/Device/LowLevel/MassStorage/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/Mouse/Doxygen.conf b/Demos/Device/LowLevel/Mouse/Doxygen.conf
index 9e8e15ec59d..704e17d79ac 100644
--- a/Demos/Device/LowLevel/Mouse/Doxygen.conf
+++ b/Demos/Device/LowLevel/Mouse/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf b/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
index d76cbe07266..48a04723b20 100644
--- a/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
+++ b/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Device/LowLevel/USBtoSerial/Doxygen.conf b/Demos/Device/LowLevel/USBtoSerial/Doxygen.conf
index 7564c95bf60..ceb4e6ad0dc 100644
--- a/Demos/Device/LowLevel/USBtoSerial/Doxygen.conf
+++ b/Demos/Device/LowLevel/USBtoSerial/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/ClassDriver/CDCHost/Doxygen.conf b/Demos/Host/ClassDriver/CDCHost/Doxygen.conf
index 45ceeeb4936..3f2e0b92036 100644
--- a/Demos/Host/ClassDriver/CDCHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/CDCHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/CDCHost/Doxygen.conf b/Demos/Host/LowLevel/CDCHost/Doxygen.conf
index 45ceeeb4936..3f2e0b92036 100644
--- a/Demos/Host/LowLevel/CDCHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/CDCHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf b/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
index c40d4d99b1d..f9cbfada69c 100644
--- a/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf b/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
index 95ffa1b05d6..c2cc231b8fe 100644
--- a/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
index 8f8744d9510..ed95d9fc184 100644
--- a/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf b/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
index 5e80f5a1b17..cdb806fb4e4 100644
--- a/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/MouseHost/Doxygen.conf b/Demos/Host/LowLevel/MouseHost/Doxygen.conf
index f57071bc2b9..a797ddc2f5b 100644
--- a/Demos/Host/LowLevel/MouseHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MouseHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
index c92fb0d11c6..62dc94ca054 100644
--- a/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/PrinterHost/Doxygen.conf b/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
index e2ee0d59ad8..ac6ed02eca6 100644
--- a/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/Host/LowLevel/StillImageHost/Doxygen.conf b/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
index 684f56287b0..f92adaadbb5 100644
--- a/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Demos/OTG/TestApp/Doxygen.conf b/Demos/OTG/TestApp/Doxygen.conf
index 1b6f4fe100b..4103510d7c1 100644
--- a/Demos/OTG/TestApp/Doxygen.conf
+++ b/Demos/OTG/TestApp/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/LUFA.pnproj b/LUFA.pnproj
index 2e725a79100..0aa5673672a 100644
--- a/LUFA.pnproj
+++ b/LUFA.pnproj
@@ -1 +1 @@
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\ No newline at end of file
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path="LUFA\Drivers\USB\Class\Device\HID.c"></File><File path="LUFA\Drivers\USB\Class\Device\HID.h"></File><File path="LUFA\Drivers\USB\Class\Device\CDC.c"></File><File path="LUFA\Drivers\USB\Class\Device\CDC.h"></File><File path="LUFA\Drivers\USB\Class\Device\RNDIS.c"></File><File path="LUFA\Drivers\USB\Class\Device\RNDIS.h"></File><File path="LUFA\Drivers\USB\Class\Device\RNDISConstants.h"></File><File path="LUFA\Drivers\USB\Class\Device\MassStorage.c"></File><File path="LUFA\Drivers\USB\Class\Device\MassStorage.h"></File><File path="LUFA\Drivers\USB\Class\Device\Audio.c"></File><File path="LUFA\Drivers\USB\Class\Device\Audio.h"></File><File path="LUFA\Drivers\USB\Class\Device\MIDI.c"></File><File path="LUFA\Drivers\USB\Class\Device\MIDI.h"></File></Folder><Folder name="Host"><File path="LUFA\Drivers\USB\Class\Host\HIDParser.c"></File><File path="LUFA\Drivers\USB\Class\Host\HIDParser.h"></File><File path="LUFA\Drivers\USB\Class\Host\HIDReportData.h"></File><File path="LUFA\Drivers\USB\Class\Host\CDC.c"></File><File path="LUFA\Drivers\USB\Class\Host\CDC.h"></File><File path="LUFA\Drivers\USB\Class\Host\HID.c"></File><File path="LUFA\Drivers\USB\Class\Host\HID.h"></File><File path="LUFA\Drivers\USB\Class\Host\Audio.c"></File><File path="LUFA\Drivers\USB\Class\Host\Audio.h"></File><File path="LUFA\Drivers\USB\Class\Host\MIDI.c"></File><File path="LUFA\Drivers\USB\Class\Host\MIDI.h"></File><File path="LUFA\Drivers\USB\Class\Host\MassStorage.c"></File><File path="LUFA\Drivers\USB\Class\Host\MassStorage.h"></File><File path="LUFA\Drivers\USB\Class\Host\StillImage.c"></File><File path="LUFA\Drivers\USB\Class\Host\StillImage.h"></File></Folder><Folder name="Common"><File path="LUFA\Drivers\USB\Class\Common\Audio.h"></File><File path="LUFA\Drivers\USB\Class\Common\CDC.h"></File><File path="LUFA\Drivers\USB\Class\Common\HID.h"></File><File path="LUFA\Drivers\USB\Class\Common\MassStorage.h"></File><File path="LUFA\Drivers\USB\Class\Common\MIDI.h"></File><File path="LUFA\Drivers\USB\Class\Common\RNDIS.h"></File><File path="LUFA\Drivers\USB\Class\Common\StillImage.h"></File></Folder><File path="LUFA\Drivers\USB\Class\Audio.h"></File><File path="LUFA\Drivers\USB\Class\CDC.h"></File><File path="LUFA\Drivers\USB\Class\HID.h"></File><File path="LUFA\Drivers\USB\Class\MassStorage.h"></File><File path="LUFA\Drivers\USB\Class\MIDI.h"></File><File path="LUFA\Drivers\USB\Class\RNDIS.h"></File><File path="LUFA\Drivers\USB\Class\StillImage.h"></File></Folder><File path="LUFA\Drivers\USB\USB.h"></File></Folder><Folder name="Misc"><File path="LUFA\Drivers\Misc\TerminalCodes.h"></File></Folder><Folder name="Board"><Folder name="USBKEY"><File path="LUFA\Drivers\Board\USBKEY\Dataflash.h"></File><File path="LUFA\Drivers\Board\USBKEY\Joystick.h"></File><File path="LUFA\Drivers\Board\USBKEY\AT45DB642D.h"></File><File path="LUFA\Drivers\Board\USBKEY\LEDs.h"></File><File path="LUFA\Drivers\Board\USBKEY\Buttons.h"></File></Folder><Folder name="STK526"><File path="LUFA\Drivers\Board\STK526\Dataflash.h"></File><File path="LUFA\Drivers\Board\STK526\Joystick.h"></File><File path="LUFA\Drivers\Board\STK526\AT45DB642D.h"></File><File path="LUFA\Drivers\Board\STK526\LEDs.h"></File><File path="LUFA\Drivers\Board\STK526\Buttons.h"></File></Folder><Folder name="STK525"><File path="LUFA\Drivers\Board\STK525\Dataflash.h"></File><File path="LUFA\Drivers\Board\STK525\Joystick.h"></File><File path="LUFA\Drivers\Board\STK525\AT45DB321C.h"></File><File path="LUFA\Drivers\Board\STK525\LEDs.h"></File><File path="LUFA\Drivers\Board\STK525\Buttons.h"></File></Folder><Folder name="RZUSBSTICK"><File path="LUFA\Drivers\Board\RZUSBSTICK\LEDs.h"></File></Folder><Folder name="ATAVRUSBRF01"><File path="LUFA\Drivers\Board\ATAVRUSBRF01\LEDs.h"></File><File path="LUFA\Drivers\Board\ATAVRUSBRF01\Buttons.h"></File></Folder><File path="LUFA\Drivers\Board\Temperature.h"></File><File path="LUFA\Drivers\Board\Dataflash.h"></File><File path="LUFA\Drivers\Board\Joystick.h"></File><File path="LUFA\Drivers\Board\Temperature.c"></File><File path="LUFA\Drivers\Board\LEDs.h"></File><File path="LUFA\Drivers\Board\Buttons.h"></File></Folder><Folder name="Peripheral"><Folder name="AT90USBXXX67"><File path="LUFA\Drivers\Peripheral\AT90USBXXX67\ADC.h"></File></Folder><File path="LUFA\Drivers\Peripheral\ADC.h"></File><File path="LUFA\Drivers\Peripheral\Serial.c"></File><File path="LUFA\Drivers\Peripheral\Serial.h"></File><File path="LUFA\Drivers\Peripheral\SPI.h"></File><File path="LUFA\Drivers\Peripheral\SerialStream.c"></File><File path="LUFA\Drivers\Peripheral\SerialStream.h"></File></Folder></Folder><Folder name="DriverStubs"><File path="LUFA\DriverStubs\Dataflash.h"></File><File path="LUFA\DriverStubs\Joystick.h"></File><File path="LUFA\DriverStubs\LEDs.h"></File><File path="LUFA\DriverStubs\Buttons.h"></File></Folder><Folder name="ManPages"><File path="LUFA\ManPages\AboutLUFA.txt"></File><File path="LUFA\ManPages\BuildingLinkableLibraries.txt"></File><File path="LUFA\ManPages\ChangeLog.txt"></File><File path="LUFA\ManPages\CompileTimeTokens.txt"></File><File path="LUFA\ManPages\DevelopingWithLUFA.txt"></File><File path="LUFA\ManPages\DeviceSupport.txt"></File><File path="LUFA\ManPages\DirectorySummaries.txt"></File><File path="LUFA\ManPages\Donating.txt"></File><File path="LUFA\ManPages\FutureChanges.txt"></File><File path="LUFA\ManPages\GettingStarted.txt"></File><File path="LUFA\ManPages\Groups.txt"></File><File path="LUFA\ManPages\LibraryResources.txt"></File><File path="LUFA\ManPages\LUFAPoweredProjects.txt"></File><File path="LUFA\ManPages\MainPage.txt"></File><File path="LUFA\ManPages\MigrationInformation.txt"></File><File path="LUFA\ManPages\VIDAndPIDValues.txt"></File><File path="LUFA\ManPages\WritingBoardDrivers.txt"></File><File path="LUFA\ManPages\ConfiguringApps.txt"></File><File path="LUFA\ManPages\CompilingApps.txt"></File><File path="LUFA\ManPages\ProgrammingApps.txt"></File><File path="LUFA\ManPages\LibraryApps.txt"></File><File path="LUFA\ManPages\Licence.txt"></File></Folder><Folder name="Scheduler"><File path="LUFA\Scheduler\Scheduler.c"></File><File path="LUFA\Scheduler\Scheduler.h"></File></Folder><File path="LUFA\makefile"></File><File path="LUFA\Version.h"></File><File path="LUFA\Doxygen.conf"></File></Folder><Folder name="Projects"><Folder name="MagStripe"><Folder name="Lib"><File path="Projects\Magstripe\Lib\CircularBitBuffer.c"></File><File path="Projects\Magstripe\Lib\CircularBitBuffer.h"></File><File path="Projects\Magstripe\Lib\MagstripeHW.h"></File></Folder><File path="Projects\Magstripe\Descriptors.c"></File><File path="Projects\Magstripe\Descriptors.h"></File><File path="Projects\Magstripe\Magstripe.c"></File><File path="Projects\Magstripe\Magstripe.h"></File><File path="Projects\Magstripe\makefile"></File><File path="Projects\Magstripe\Magstripe.txt"></File><File path="Projects\Magstripe\Doxygen.conf"></File></Folder><Folder name="MissileLauncher"><File path="Projects\MissileLauncher\ConfigDescriptor.c"></File><File path="Projects\MissileLauncher\ConfigDescriptor.h"></File><File path="Projects\MissileLauncher\Doxygen.conf"></File><File path="Projects\MissileLauncher\makefile"></File><File path="Projects\MissileLauncher\MissileLauncher.c"></File><File path="Projects\MissileLauncher\MissileLauncher.h"></File><File path="Projects\MissileLauncher\MissileLauncher.txt"></File></Folder><File path="Projects\makefile"></File></Folder><Folder name="Bootloaders"><Folder name="DFU"><File path="Bootloaders\DFU\BootloaderDFU.c"></File><File path="Bootloaders\DFU\BootloaderDFU.h"></File><File path="Bootloaders\DFU\Descriptors.c"></File><File path="Bootloaders\DFU\Descriptors.h"></File><File path="Bootloaders\DFU\makefile"></File><File path="Bootloaders\DFU\BootloaderDFU.txt"></File><File path="Bootloaders\DFU\Doxygen.conf"></File></Folder><Folder name="CDC"><File path="Bootloaders\CDC\BootloaderCDC.c"></File><File path="Bootloaders\CDC\BootloaderCDC.h"></File><File path="Bootloaders\CDC\Descriptors.c"></File><File path="Bootloaders\CDC\Descriptors.h"></File><File path="Bootloaders\CDC\makefile"></File><File path="Bootloaders\CDC\LUFA CDC Bootloader.inf"></File><File path="Bootloaders\CDC\Doxygen.conf"></File><File path="Bootloaders\CDC\BootloaderCDC.txt"></File></Folder><Folder name="TeensyHID"><File path="Bootloaders\TeensyHID\Descriptors.c"></File><File path="Bootloaders\TeensyHID\Descriptors.h"></File><File path="Bootloaders\TeensyHID\makefile"></File><File path="Bootloaders\TeensyHID\TeensyHID.c"></File><File path="Bootloaders\TeensyHID\TeensyHID.h"></File><File path="Bootloaders\TeensyHID\TeensyHID.txt"></File></Folder><File path="Bootloaders\makefile"></File></Folder><File path="makefile"></File><File path="README.txt"></File></Project>
\ No newline at end of file
diff --git a/LUFA/Doxygen.conf b/LUFA/Doxygen.conf
index 76a55c8f29b..260340c054b 100644
--- a/LUFA/Doxygen.conf
+++ b/LUFA/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Projects/Magstripe/Doxygen.conf b/Projects/Magstripe/Doxygen.conf
index b959ff8b68b..4f1a3875300 100644
--- a/Projects/Magstripe/Doxygen.conf
+++ b/Projects/Magstripe/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/Projects/MissileLauncher/Doxygen.conf b/Projects/MissileLauncher/Doxygen.conf
index c40d4d99b1d..f9cbfada69c 100644
--- a/Projects/MissileLauncher/Doxygen.conf
+++ b/Projects/MissileLauncher/Doxygen.conf
@@ -47,7 +47,7 @@ OUTPUT_DIRECTORY       = ./Documentation/
 # source files, where putting all generated files in the same directory would 
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
diff --git a/makefile b/makefile
index 1887e5afc45..b087f9b0f20 100644
--- a/makefile
+++ b/makefile
@@ -6,12 +6,12 @@
 #      www.fourwalledcubicle.com
 #
 
-# Makefile to build the LUFA library and Demos.
+# Makefile to build the LUFA library, projects and demos.
 
 # Call with "make all" to rebuild everything, "make clean" to clean everything,
 # "make clean_list" to remove all intermediatary files but preserve any binaries,
-# "make doxygen" to document the library/demos/etc. with DoxyGen (if installed) and
-# "make clean_doxygen" to remove generated Doxygen documentation.
+# "make doxygen" to document everything with DoxyGen (if installed) and
+# "make clean_doxygen" to remove generated Doxygen documentation from everything.
 
 # It is suggested that for the master build, the --quiet switch is passed to make,
 # to remove all the commands from the output. This gives a much easier to read