diff --git a/LUFA.pnproj b/LUFA.pnproj
index 870cf4cf08..b528f388b5 100644
--- a/LUFA.pnproj
+++ b/LUFA.pnproj
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/Projects/LEDNotifier/Doxygen.conf b/Projects/LEDNotifier/Doxygen.conf
index 432339e64d..d779972587 100644
--- a/Projects/LEDNotifier/Doxygen.conf
+++ b/Projects/LEDNotifier/Doxygen.conf
@@ -615,7 +615,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = Documentation/
+EXCLUDE                = Documentation/ CPUUsageApp/ HotmailNotifierApp/ LEDMixerApp/
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
 # directories that are symbolic links (a Unix filesystem feature) are excluded
diff --git a/Projects/TemperatureDataLogger/Doxygen.conf b/Projects/TemperatureDataLogger/Doxygen.conf
index b810dc0adf..32278385a6 100644
--- a/Projects/TemperatureDataLogger/Doxygen.conf
+++ b/Projects/TemperatureDataLogger/Doxygen.conf
@@ -615,7 +615,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = Documentation/
+EXCLUDE                = Documentation/ TempLogHostApp/
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
 # directories that are symbolic links (a Unix filesystem feature) are excluded