Update Makefile.gappkg to latest

Also remove doc/clean as it is no longer used

Makefile.gappkg

@@ -17,13 +17,6 @@
 #   KEXT_USE_AUTOCONF to 1 to enable dependency rules that enable
 #   regenerating the configure script etc. when necessary
 #
-# Only GAP >= 4.11 ships with this file. In order to keep your package
-# compatible with older GAP versions, we recommend to bundle a copy of
-# it with your package, but only as a fallback. So, your configure
-# scripts should check if GAP ships with this file, and use it then, and
-# only fall back to your own copy as a last resort. This way, you will
-# benefit from any fixes and improvements made by the GAP team.
-#
 # The contents of this file are released into the public domain; hence
 # you may edit this file as you wish, bundle and distribute it with your
 # package, etc.
@@ -46,7 +39,7 @@ ifndef GAP_KERNEL_MAJOR_VERSION
   KEXT_CXXFLAGS += -I$(GAP_LIB_DIR)/src
 endif
 
-# honor used supplied flags
+# honor user supplied flags
 KEXT_CFLAGS += $(CPPFLAGS)
 KEXT_CFLAGS += $(CFLAGS)
 KEXT_CXXFLAGS += $(CPPFLAGS)
@@ -151,7 +144,9 @@ clean-kext:
 distclean: distclean-kext
 distclean-kext:
 	rm -rf bin gen Makefile
-	(cd doc && ./clean)
+	rm -rf doc/_*.xml
+	rm -rf doc/*.aux doc/*.bbl doc/*.blg doc/*.brf doc/*.idx doc/*.idx
+	rm -rf doc/*.ilg doc/*.ind doc/*.log doc/*.out doc/*.pnr doc/*.toc
 
 # hook into `make doc`
 doc: doc-kext
@@ -193,14 +188,14 @@ gen/pkgconfig.h: gen/pkgconfig.h.stamp
 	@if test ! -f $@; then rm -f $<; else :; fi
 	@if test ! -f $@; then $(MAKE) $<; else :; fi
 
-gen/pkgconfig.h.stamp: gen/pkgconfig.h.in config.status
+gen/pkgconfig.h.stamp: src/pkgconfig.h.in config.status
 	@rm -f $@
 	@mkdir -p $(@D)
 	./config.status gen/pkgconfig.h
 	echo > $@
 
 ifneq ($(MAINTAINER_MODE),no)
-gen/pkgconfig.h.in: $(configure_deps)
+src/pkgconfig.h.in: $(configure_deps)
 	@if command -v autoheader >/dev/null 2>&1 ; then \
 	   mkdir -p $(@D) ; \
 	   echo "running autoheader" ; \