diff --git a/developer-doc/.gitignore b/developer-doc/.gitignore
index ad4cccefa7c615d8a11648649b50d960e6f0291a..9a6b1538130646a7d61100d7beb59b4c3a0d1bbc 100644
--- a/developer-doc/.gitignore
+++ b/developer-doc/.gitignore
@@ -4,5 +4,4 @@
 /automatic
 /*PP.txt
 /links-to-user-manual.txt
-/Doxyfile
 
diff --git a/developer-doc/Doxyfile.in b/developer-doc/Doxyfile
similarity index 99%
rename from developer-doc/Doxyfile.in
rename to developer-doc/Doxyfile
index 540425126bdf711579b679cc68eee9aec6303921..4ca478d7ee706dc931f6159f244da74b326ca382 100644
--- a/developer-doc/Doxyfile.in
+++ b/developer-doc/Doxyfile
@@ -738,7 +738,6 @@ INPUT                  = ./Intro.txt \
                          ./plmdIntro.txt \
                          ./usingDoxygen.txt \
                          ./parsing.txt \
-                         @SRCDIR@ \
                          ./links-to-user-manual.txt \
                          ./AddingAColvar.txt \
                          ./AddingAFunction.txt \
@@ -911,13 +910,13 @@ STRIP_CODE_COMMENTS    = NO
 # function all documented functions referencing it will be listed.
 # The default value is: NO.
 
-REFERENCED_BY_RELATION = @MAYBE@
+REFERENCED_BY_RELATION = NO
 
 # If the REFERENCES_RELATION tag is set to YES then for each documented function
 # all documented entities called/used by that function will be listed.
 # The default value is: NO.
 
-REFERENCES_RELATION    = @MAYBE@
+REFERENCES_RELATION    = NO
 
 # If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
 # to YES, then the hyperlinks from functions in REFERENCES_RELATION and
diff --git a/developer-doc/Makefile b/developer-doc/Makefile
index 4cae983e1ab1b3deb3a00697e5ed126eeee85177..5a3d7730a3ad64a3f4002dabb6602e0d8ee23f84 100644
--- a/developer-doc/Makefile
+++ b/developer-doc/Makefile
@@ -3,8 +3,8 @@
 
 all:
 	./extract
-	doxygen
+	./go-doxygen
 	cp Octocat.png html/
 
 clean:
-	rm -fr automatic html latex *~ links-to-user-manual.txt Doxyfile
+	rm -fr automatic html latex *~ links-to-user-manual.txt
diff --git a/developer-doc/extract b/developer-doc/extract
index 19a519c207f5dc8e56b223dbd87abc47d2ead4d9..b2b803f1815c2211a10c9504ec8a071f10cf9b98 100755
--- a/developer-doc/extract
+++ b/developer-doc/extract
@@ -1,8 +1,5 @@
 #!/bin/bash
 
-sed s:@SRCDIR@:"$(echo ../src/*/ ../src/*/*/)": Doxyfile.in|
-sed s:@MAYBE@:NO: > Doxyfile
-
 cat ../src/*/*cpp |
 awk '
   /PLUMED_REGISTER_ACTION/{print}
diff --git a/developer-doc/go-doxygen b/developer-doc/go-doxygen
new file mode 100755
index 0000000000000000000000000000000000000000..776ad8b84bb6a5eaa2dc3606d33d59012dc35a76
--- /dev/null
+++ b/developer-doc/go-doxygen
@@ -0,0 +1,9 @@
+#! /bin/bash
+
+{
+  cat Doxyfile
+  echo "PROJECT_NUMBER = \"$(plumed info --version)\""
+  echo "INPUT+=" ../src/*/ ../src/*/*/
+  echo "REFERENCES_RELATION=NO"
+  echo "REFERENCED_BY_RELATION=NO"
+} | doxygen -