diff --git a/guacamole-common/.gitignore b/guacamole-common/.gitignore
index 42f4a1a64..533192e5f 100644
--- a/guacamole-common/.gitignore
+++ b/guacamole-common/.gitignore
@@ -1,2 +1,10 @@
+
+# Compiled code
 target/
+
+# Backup files
 *~
+
+# Generated docs
+doc/doxygen-output
+
diff --git a/guacamole-common/Doxyfile b/guacamole-common/doc/Doxyfile
similarity index 99%
rename from guacamole-common/Doxyfile
rename to guacamole-common/doc/Doxyfile
index 339015afd..f9150ec95 100644
--- a/guacamole-common/Doxyfile
+++ b/guacamole-common/doc/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NUMBER         = 0.5.0
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = doc
+OUTPUT_DIRECTORY       = doxygen-output
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -574,7 +574,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  =
+INPUT                  = ../src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is