diff --git a/doc/doxygen.conf.in b/doc/doxygen.conf.in
index d268ea0..2d007fc 100644
--- a/doc/doxygen.conf.in
+++ b/doc/doxygen.conf.in
@@ -864,7 +864,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @TOP_SRCDIR@/src @TOP_SRCDIR@/lib @TOP_SRCDIR@/include
+INPUT                  = @TOP_SRCDIR@/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. Doxygen uses
@@ -2237,9 +2237,9 @@ SEARCH_INCLUDES        = YES
 
 INCLUDE_PATH           = @TOP_SRCDIR@/src \
                          @TOP_SRCDIR@/src/ast \
-                         @TOP_SRCDIR@/src/models \
-                         @TOP_SRCDIR@/lib \
-                         @TOP_SRCDIR@/include
+                         @TOP_SRCDIR@/src/lib \
+                         @TOP_SRCDIR@/src/lib/models \
+                         @TOP_SRCDIR@/src/lib/include
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the