diff --git a/Doxyfile.in b/Doxyfile.core.in
similarity index 100%
rename from Doxyfile.in
rename to Doxyfile.core.in
diff --git a/Makefile.am b/Makefile.am
index f5c6be7..e1bf86f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -29,10 +29,10 @@
 		  $(top_builddir)/doc/codec/html/index.html
 	cd $(top_builddir)/doc && tar cf html.tar */html
 
-$(top_builddir)/doc/core/html/index.html: $(SOURCES) Doxyfile
+$(top_builddir)/doc/core/html/index.html: $(SOURCES) Doxyfile.core
 	@rm -rf doc/core
 	mkdir -p doc/core
-	$(DOXYGEN) Doxyfile
+	$(DOXYGEN) Doxyfile.core
 
 $(top_builddir)/doc/gsm/html/index.html: $(SOURCES) Doxyfile.gsm
 	@rm -rf doc/gsm
@@ -53,6 +53,6 @@
 	cd $(DESTDIR)$(doc_htmldir) && tar xf html.tar && rm -f html.tar
 
 uninstall-hook:
-	cd $(DESTDIR)$(doc_htmldir) && rm -rf *
+	cd $(DESTDIR)$(doc_htmldir) && rm -rf {core,gsm,vty,codec}
 
 endif
diff --git a/configure.ac b/configure.ac
index a77e3e8..ef4b0aa 100644
--- a/configure.ac
+++ b/configure.ac
@@ -124,7 +124,7 @@
 	tests/ussd/Makefile
 	tests/smscb/Makefile
 	utils/Makefile
-	Doxyfile
+	Doxyfile.core
 	Doxyfile.gsm
 	Doxyfile.vty
 	Doxyfile.codec