diff --git a/Makefile b/Makefile
index 4a8af8f82..a33ecbcf0 100644
--- a/Makefile
+++ b/Makefile
@@ -39,3 +39,6 @@ install:
 	(cd server; make DEST=$(DEST) install)
 	(cd log_manager; make DEST=$(DEST) install)
 	(cd query_classifier; make DEST=$(DEST) install)
+
+documentation:
+	doxygen doxygate
diff --git a/doxygate b/doxygate
index 55ab2c5ac..5737db509 100644
--- a/doxygate
+++ b/doxygate
@@ -568,7 +568,8 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = README core modules include
+INPUT                  = README server/core server/modules server/include \
+			log_manager query_classifier utils
 
 # 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
diff --git a/server/Makefile b/server/Makefile
index 8a483162a..5c9a74027 100644
--- a/server/Makefile
+++ b/server/Makefile
@@ -47,9 +47,6 @@ depend:
 	(cd modules/protocol; touch depend.mk ; make depend)
 	(cd modules/monitor; touch depend.mk ; make depend)
 
-documentation:
-	doxygen doxygate
-
 install:
 	@mkdir -p $(DEST)
 	@mkdir -p $(DEST)/MaxScale