diff --git a/Makefile.in b/Makefile.in
index 3e0c773a8..da74f1fd6 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -23,7 +23,7 @@
 #
 # Makefile for the fish shell. Can build fish and associated
 # applications, install them, recalculate dependencies and also create
-# binary distributions in tar.bz2 tar.gz and rpm formats.
+# binary distributions in tar.bz2, tar.gz and rpm formats.
 #
 
 #
@@ -56,44 +56,36 @@ ETC_DIR_INSTALL = etc/fish_interactive.fish
 # Set to 1 if we have gettext
 HAVE_GETTEXT=@HAVE_GETTEXT@
 
-CORE_OBJS := util.o common.o halloc.o halloc_util.o fallback.o
+#Additional .c files used by common.o. These also have a corresponding
+#.h file.
+COMMON_FILES := util.c halloc.c halloc_util.c fallback.c
 
-# All objects used by fish, that are compiled from an ordinary .c file
-# using an ordinary .h file.
-COMMON_OBJS := function.o builtin.o complete.o env.o exec.o	\
+# All objects that the system needs to build fish, except main.o
+FISH_OBJS := function.o builtin.o complete.o env.o exec.o	\
 	expand.o highlight.o history.o kill.o parser.o proc.o reader.o		\
 	sanity.o tokenizer.o wildcard.o wgetopt.o wutil.o input.o	\
 	output.o intern.o env_universal.o env_universal_common.o			\
-	input_common.o event.o signal.o io.o translate.o parse_util.o		\
-	$(CORE_OBJS)
+	input_common.o event.o signal.o io.o translate.o parse_util.o common.o \
 
-# builtin_help.h exists, but builtin_help.c is autogenerated
-COMMON_OBJS_WITH_HEADER := builtin_help.o
-
-# main.c exists, but main.h does not, etc.
-COMMON_OBJS_WITH_CODE := builtin_set.o builtin_commandline.o	\
-	builtin_ulimit.o builtin_complete.o builtin_jobs.o
-
-# All objects that the system needs to build fish
-FISH_OBJS := $(COMMON_OBJS) $(COMMON_OBJS_WITH_CODE)	\
-	$(COMMON_OBJS_WITH_HEADER) main.o
+# Additional files used by builtin.o
+BUILTIN_FILES := builtin_help.c builtin_set.c builtin_commandline.c	\
+	builtin_ulimit.c builtin_complete.c builtin_jobs.c
 
 # All objects that the system needs to build fish_pager
 FISH_PAGER_OBJS := fish_pager.o output.o wutil.o		\
 	tokenizer.o input_common.o env_universal.o env_universal_common.o	\
-	translate.o $(CORE_OBJS)
+	translate.o common.o
 
 # All objects that the system needs to build fish_tests
-FISH_TESTS_OBJS := $(COMMON_OBJS) $(COMMON_OBJS_WITH_CODE)	\
-	$(COMMON_OBJS_WITH_HEADER) fish_tests.o
+FISH_TESTS_OBJS := common.o fish_tests.o
 
 # All objects that the system needs to build fishd
 FISHD_OBJS := fishd.o env_universal_common.o wutil.o	\
-	doc_src/fishd.o $(CORE_OBJS)
+	doc_src/fishd.o common.o
 
 # All objects needed to build mimedb
 MIME_OBJS := mimedb.o xdgmimealias.o xdgmime.o xdgmimeglob.o		\
-	xdgmimeint.o xdgmimemagic.o xdgmimeparent.o wutil.o $(CORE_OBJS)
+	xdgmimeint.o xdgmimemagic.o xdgmimeparent.o wutil.o common.o
 
 #
 # Files containing documentation for builtins. Should be listed
@@ -150,14 +142,14 @@ DOC_SRC_DIR_FILES := doc_src/Doxyfile.in doc_src/doc.hdr	\
 	$(BUILTIN_DOC_SRC) $(CMD_DOC_SRC) doc_src/fish.1.in
 
 # Files in ./
-MAIN_DIR_FILES := Doxyfile Doxyfile.user Makefile.in configure			\
-    configure.ac config.h.in install-sh set_color.c count.c				\
-    key_reader.c gen_hdr.sh gen_hdr2.c $(MIME_OBJS:.o=.h)				\
-    $(MIME_OBJS:.o=.c) $(COMMON_OBJS_WITH_HEADER:.o=.h)					\
-    $(COMMON_OBJS:.o=.h) $(COMMON_OBJS_WITH_CODE:.o=.c)					\
-    $(COMMON_OBJS:.o=.c) builtin_help.hdr fish.spec.in INSTALL README	\
-    user_doc.head.html xsel-0.9.6.tar ChangeLog config.sub				\
-    config.guess fish_tests.c main.c fish_pager.c fishd.c seq.in
+MAIN_DIR_FILES := Doxyfile Doxyfile.user Makefile.in configure		\
+    configure.ac config.h.in install-sh set_color.c count.c			\
+    key_reader.c gen_hdr.sh gen_hdr2.c $(MIME_OBJS:.o=.h)			\
+    $(MIME_OBJS:.o=.c) $(FISH_OBJS:.o=.h) $(BUILTIN_FILES)			\
+    $(COMMON_FILES) $(COMMON_FILES:.c=.h) $(FISH_OBJS:.o=.c)		\
+    builtin_help.hdr fish.spec.in INSTALL README user_doc.head.html	\
+    xsel-0.9.6.tar ChangeLog config.sub config.guess fish_tests.c	\
+    main.c fish_pager.c fishd.c seq.in
 
 # Files in ./etc/
 ETC_DIR_FILES :=etc/fish.in etc/fish_inputrc	\
@@ -208,8 +200,10 @@ debug:
 .PHONY: debug
 
 # User documentation, describing the features of the fish shell.
-user_doc: doc.h Doxyfile.user user_doc.head.html
+user_doc: doc_src/doc.hdr Doxyfile.user user_doc.head.html
+	$(MAKE) doc.h # Depend on the source (doc.hdr) and manually make the intermediate as needed
 	doxygen Doxyfile.user
+	touch user_doc
 
 # Source code documentation. Also includes user documentation.
 doc: *.h *.c doc.h Doxyfile builtin_help.c
@@ -283,6 +277,10 @@ messages.pot: *.c *.h etc/*.in share/fish share/completions/*.fish share/functio
 		fi; \
 	fi
 
+builtin.o: $(BUILTIN_FILES)
+
+common.o: $(COMMON_FILES)
+
 # Generate the internal help functions by making doxygen create
 # man-pages which are then converted into C code. The convertion path
 # looks like this: 
@@ -315,15 +313,24 @@ messages.pot: *.c *.h etc/*.in share/fish share/completions/*.fish share/functio
 # Which is an awful, clunky and ugly way of producing
 # documentation. There ought to be something simpler.
 
-builtin_help.c: $(BUILTIN_DOC_HDR) doc_src/count.doxygen gen_hdr2 gen_hdr.sh builtin_help.hdr $(CMD_DOC_HDR)
-	cd doc_src; doxygen; cd ..; 
+doc_src/builtin_doc: $(BUILTIN_DOC_SRC) doc_src/count.txt builtin_help.hdr $(CMD_DOC_SRC)
+	for i in $(BUILTIN_DOC_SRC) $(CMD_DOC_SRC); do \
+		FILE=doc_src/`basename $$i .txt`.doxygen; \
+		echo  "/** \page" `basename $$i .txt` >$$FILE; \
+		cat $$i >>$$FILE; \
+		echo "*/" >>$$FILE; \
+	done
+	cd doc_src; doxygen; cd ..;
+	touch doc_src/builtin_doc
+
+builtin_help.c: doc_src/builtin_doc gen_hdr.sh
+	$(MAKE) gen_hdr2 # Don't depend on gen_hdr2, because then we would need to rebuild the docs whenever we use a fresh tarball
 	cp builtin_help.hdr builtin_help.c; 
-	chmod 755 gen_hdr.sh
+	if ! test -x gen_hdr.sh; then chmod 755 gen_hdr.sh; fi
 	for i in $(BUILTIN_DOC_HDR) doc_src/count.doxygen ; do \
-		echo '    hash_put( &tbl, L"'`basename $$i .doxygen`'",' >>$@; \
+		echo '	hash_put( &tbl, L"'`basename $$i .doxygen`'",' >>$@; \
 		./gen_hdr.sh $$i >>$@; \
-		echo " );" >>$@; \
-		echo >>$@; \
+		printf " );\n\n" >>$@; \
 	done;
 	echo "}" >>builtin_help.c
 
@@ -332,7 +339,8 @@ builtin_help.c: $(BUILTIN_DOC_HDR) doc_src/count.doxygen gen_hdr2 gen_hdr.sh bui
 # mimedb. Depends on builtin_help.c to make sure doxygen gets run to
 # generate the man files.
 #
-%.c : %.doxygen gen_hdr2 builtin_help.c
+%.c : %.doxygen 
+	$(MAKE) gen_hdr2 builtin_help.c # These should really be filed as dependencis for %.c above instead, but that seems to confuse make
 	echo "// This file was automatically generated, do not edit" >$@
 	echo "#include <stdlib.h>" >>$@
 	echo "#include <stdio.h>" >>$@
@@ -478,8 +486,8 @@ uninstall-translations:
 # The build rules for all the commands
 #
 
-fish: $(FISH_OBJS) 
-	$(CC) $(FISH_OBJS) $(LDFLAGS) -o $@
+fish: $(FISH_OBJS) main.o 
+	$(CC) $(FISH_OBJS) main.o $(LDFLAGS) -o $@
 
 fish_pager: $(FISH_PAGER_OBJS)
 	$(CC) $(FISH_PAGER_OBJS) $(LDFLAGS) -o $@
@@ -498,12 +506,12 @@ set_color: set_color.o doc_src/set_color.o
 	$(CC) set_color.o doc_src/set_color.o $(LDFLAGS) -o $@
 
 # Test program for the tokenizer library
-tokenizer_test: tokenizer.c tokenizer.h util.o wutil.o common.o
-	$(CC) ${CFLAGS} tokenizer.c util.o wutil.o common.o -D TOKENIZER_TEST $(LDFLAGS) -o $@
+tokenizer_test: tokenizer.c tokenizer.h wutil.o common.o
+	$(CC) ${CFLAGS} tokenizer.c wutil.o common.o -D TOKENIZER_TEST $(LDFLAGS) -o $@
 
 # Neat little program to show output from terminal
-key_reader: key_reader.o input_common.o $(CORE_OBJS) env_universal.o env_universal_common.o wutil.o
-	$(CC) key_reader.o input_common.o $(CORE_OBJS) env_universal.o env_universal_common.o wutil.o $(LDFLAGS) -o $@
+key_reader: key_reader.o input_common.o common.o env_universal.o env_universal_common.o wutil.o
+	$(CC) key_reader.o input_common.o common.o env_universal.o env_universal_common.o wutil.o $(LDFLAGS) -o $@
 
 #
 # Update dependencies
@@ -519,7 +527,7 @@ depend:
 #
 # Uses install instead of mkdir so build won't fail if the directory 
 # exists
-fish-@PACKAGE_VERSION@.tar: $(DOC_SRC_DIR_FILES) $(MAIN_DIR_FILES) $(ETC_DIR_FILES) $(TEST_DIR_FILES) $(SHARE_DIR_FILES) $(FUNCTIONS_DIR_FILES) $(COMPLETIONS_DIR_FILES) ChangeLog user_doc
+fish-@PACKAGE_VERSION@.tar: $(DOC_SRC_DIR_FILES) $(MAIN_DIR_FILES) $(ETC_DIR_FILES) $(TEST_DIR_FILES) $(SHARE_DIR_FILES) $(FUNCTIONS_DIR_FILES) $(COMPLETIONS_DIR_FILES) ChangeLog user_doc doc_src/builtin_doc
 	rm -rf fish-@PACKAGE_VERSION@
 	$(INSTALL) -d fish-@PACKAGE_VERSION@
 	$(INSTALL) -d fish-@PACKAGE_VERSION@/doc_src
@@ -531,7 +539,6 @@ fish-@PACKAGE_VERSION@.tar: $(DOC_SRC_DIR_FILES) $(MAIN_DIR_FILES) $(ETC_DIR_FIL
 	$(INSTALL) -d fish-@PACKAGE_VERSION@/tests
 	$(INSTALL) -d fish-@PACKAGE_VERSION@/po
 	cp -f $(DOC_SRC_DIR_FILES) fish-@PACKAGE_VERSION@/doc_src
-	cp -rf user_doc fish-@PACKAGE_VERSION@/
 	cp -f $(MAIN_DIR_FILES) fish-@PACKAGE_VERSION@/
 	cp -f $(ETC_DIR_FILES) fish-@PACKAGE_VERSION@/etc/
 	cp -f $(SHARE_DIR_FILES) fish-@PACKAGE_VERSION@/share/
@@ -539,6 +546,8 @@ fish-@PACKAGE_VERSION@.tar: $(DOC_SRC_DIR_FILES) $(MAIN_DIR_FILES) $(ETC_DIR_FIL
 	cp -f $(FUNCTIONS_DIR_FILES) fish-@PACKAGE_VERSION@/share/functions/
 	cp -f $(TESTS_DIR_FILES) fish-@PACKAGE_VERSION@/tests/
 	cp -f $(TRANSLATIONS_SRC) fish-@PACKAGE_VERSION@/po/
+	cp -rf user_doc fish-@PACKAGE_VERSION@/
+	cp -rf doc_src/builtin_doc fish-@PACKAGE_VERSION@/doc_src/
 	tar -c fish-@PACKAGE_VERSION@ >fish-@PACKAGE_VERSION@.tar
 	rm -rf fish-@PACKAGE_VERSION@
 
@@ -598,112 +607,116 @@ clean:
 
 # DO NOT DELETE THIS LINE -- make depend depends on it.
 
-builtin.o: config.h fallback.h common.h util.h wutil.h builtin.h function.h
-builtin.o: complete.h proc.h io.h parser.h event.h reader.h env.h wgetopt.h
-builtin.o: sanity.h tokenizer.h builtin_help.h wildcard.h input_common.h
-builtin.o: input.h intern.h signal.h translate.h halloc.h halloc_util.h
-builtin.o: parse_util.h expand.h
-builtin_commandline.o: signal.h config.h fallback.h common.h util.h wutil.h
-builtin_commandline.o: builtin.h wgetopt.h reader.h proc.h io.h parser.h
+builtin.o: config.h fallback.h util.h wutil.h builtin.h function.h complete.h
+builtin.o: proc.h io.h parser.h event.h reader.h env.h common.h wgetopt.h
+builtin.o: sanity.h tokenizer.h wildcard.h input_common.h input.h intern.h
+builtin.o: signal.h translate.h halloc.h halloc_util.h parse_util.h expand.h
+builtin.o: builtin_help.c builtin_set.c builtin_commandline.c
+builtin.o: builtin_complete.c builtin_ulimit.c builtin_jobs.c
+builtin_commandline.o: signal.h config.h fallback.h util.h wutil.h builtin.h
+builtin_commandline.o: common.h wgetopt.h reader.h proc.h io.h parser.h
 builtin_commandline.o: event.h tokenizer.h input_common.h input.h translate.h
 builtin_commandline.o: parse_util.h
-builtin_complete.o: signal.h config.h fallback.h common.h util.h wutil.h
-builtin_complete.o: builtin.h complete.h wgetopt.h parser.h proc.h io.h
+builtin_complete.o: signal.h config.h fallback.h util.h wutil.h builtin.h
+builtin_complete.o: common.h complete.h wgetopt.h parser.h proc.h io.h
 builtin_complete.o: event.h reader.h translate.h
-builtin_help.o: config.h util.h common.h builtin_help.h
-builtin_set.o: signal.h config.h fallback.h common.h util.h wutil.h builtin.h
-builtin_set.o: env.h expand.h wgetopt.h proc.h io.h parser.h event.h
+builtin_help.o: config.h util.h common.h halloc_util.h
+builtin_jobs.o: config.h fallback.h util.h wutil.h builtin.h proc.h io.h
+builtin_jobs.o: parser.h event.h common.h wgetopt.h translate.h
+builtin_set.o: signal.h config.h fallback.h util.h wutil.h builtin.h env.h
+builtin_set.o: expand.h common.h wgetopt.h proc.h io.h parser.h event.h
 builtin_set.o: translate.h
-builtin_ulimit.o: config.h fallback.h common.h util.h builtin.h wgetopt.h
+builtin_ulimit.o: config.h fallback.h util.h builtin.h common.h wgetopt.h
 builtin_ulimit.o: translate.h
-common.o: config.h fallback.h common.h util.h wutil.h expand.h proc.h io.h
-common.o: wildcard.h parser.h event.h
-complete.o: signal.h config.h fallback.h common.h util.h tokenizer.h
-complete.o: wildcard.h proc.h io.h parser.h event.h function.h complete.h
-complete.o: builtin.h env.h exec.h expand.h reader.h history.h intern.h
-complete.o: translate.h parse_util.h halloc_util.h wutil.h
-env.o: config.h signal.h fallback.h common.h util.h wutil.h proc.h io.h env.h
+common.o: config.h fallback.h util.h wutil.h common.h expand.h proc.h io.h
+common.o: wildcard.h parser.h event.h util.c halloc.c halloc.h halloc_util.c
+common.o: fallback.c
+complete.o: signal.h config.h fallback.h util.h tokenizer.h wildcard.h proc.h
+complete.o: io.h parser.h event.h function.h complete.h builtin.h env.h
+complete.o: exec.h expand.h common.h reader.h history.h intern.h translate.h
+complete.o: parse_util.h halloc.h halloc_util.h wutil.h
+env.o: config.h signal.h fallback.h util.h wutil.h proc.h io.h common.h env.h
 env.o: sanity.h expand.h history.h reader.h parser.h event.h env_universal.h
 env.o: env_universal_common.h input_common.h translate.h complete.h
-env_universal.o: config.h signal.h fallback.h common.h util.h wutil.h
+env_universal.o: config.h signal.h fallback.h util.h common.h wutil.h
 env_universal.o: env_universal_common.h env_universal.h
-env_universal_common.o: config.h signal.h fallback.h common.h util.h wutil.h
+env_universal_common.o: config.h signal.h fallback.h util.h common.h wutil.h
 env_universal_common.o: env_universal_common.h
-event.o: signal.h config.h fallback.h common.h util.h wutil.h function.h
-event.o: proc.h io.h parser.h event.h translate.h halloc_util.h
-exec.o: signal.h config.h fallback.h common.h util.h wutil.h proc.h io.h
+event.o: signal.h config.h fallback.h util.h wutil.h function.h proc.h io.h
+event.o: parser.h event.h common.h translate.h halloc_util.h
+exec.o: signal.h config.h fallback.h util.h common.h wutil.h proc.h io.h
 exec.o: exec.h parser.h event.h builtin.h function.h env.h wildcard.h
 exec.o: sanity.h expand.h env_universal.h env_universal_common.h translate.h
 exec.o: halloc.h halloc_util.h parse_util.h
-expand.o: signal.h config.h fallback.h common.h util.h wutil.h env.h proc.h
+expand.o: signal.h config.h fallback.h util.h common.h wutil.h env.h proc.h
 expand.o: io.h parser.h event.h expand.h wildcard.h exec.h tokenizer.h
 expand.o: complete.h translate.h parse_util.h halloc_util.h
-fallback.o: config.h fallback.h common.h util.h
-fishd.o: config.h signal.h fallback.h common.h util.h wutil.h
+fallback.o: config.h fallback.h util.h
+fishd.o: config.h signal.h fallback.h util.h common.h wutil.h
 fishd.o: env_universal_common.h
-fish_pager.o: config.h signal.h fallback.h common.h util.h wutil.h complete.h
+fish_pager.o: config.h signal.h fallback.h util.h wutil.h common.h complete.h
 fish_pager.o: output.h input_common.h env_universal.h env_universal_common.h
 fish_pager.o: halloc.h halloc_util.h
-fish_tests.o: config.h signal.h fallback.h common.h util.h proc.h io.h
+fish_tests.o: config.h signal.h fallback.h util.h common.h proc.h io.h
 fish_tests.o: reader.h builtin.h function.h complete.h wutil.h env.h expand.h
 fish_tests.o: parser.h event.h tokenizer.h output.h exec.h halloc_util.h
-function.o: signal.h config.h wutil.h fallback.h common.h util.h function.h
-function.o: proc.h io.h translate.h parser.h event.h intern.h reader.h
+function.o: signal.h config.h wutil.h fallback.h util.h function.h proc.h
+function.o: io.h translate.h parser.h event.h common.h intern.h reader.h
 function.o: parse_util.h env.h expand.h
-halloc.o: config.h fallback.h common.h util.h halloc.h
-halloc_util.o: config.h fallback.h common.h util.h halloc.h
-highlight.o: signal.h config.h fallback.h common.h util.h wutil.h highlight.h
+halloc.o: config.h fallback.h util.h common.h halloc.h
+halloc_util.o: config.h fallback.h util.h common.h halloc.h
+highlight.o: signal.h config.h fallback.h util.h wutil.h highlight.h
 highlight.o: tokenizer.h proc.h io.h parser.h event.h parse_util.h builtin.h
-highlight.o: function.h env.h expand.h sanity.h complete.h output.h
-history.o: config.h fallback.h common.h util.h wutil.h history.h reader.h
+highlight.o: function.h env.h expand.h sanity.h common.h complete.h output.h
+highlight.o: halloc.h halloc_util.h
+history.o: config.h fallback.h util.h wutil.h history.h common.h reader.h
 history.o: env.h sanity.h signal.h
-input.o: config.h signal.h fallback.h common.h util.h wutil.h reader.h proc.h
-input.o: io.h sanity.h input_common.h input.h parser.h event.h env.h expand.h
-input.o: translate.h output.h
-input_common.o: config.h fallback.h common.h util.h wutil.h input_common.h
+input.o: config.h signal.h fallback.h util.h wutil.h reader.h proc.h io.h
+input.o: common.h sanity.h input_common.h input.h parser.h event.h env.h
+input.o: expand.h translate.h output.h
+input_common.o: config.h fallback.h util.h common.h wutil.h input_common.h
 input_common.o: env_universal.h env_universal_common.h
-intern.o: config.h fallback.h common.h util.h wutil.h intern.h
-io.o: config.h fallback.h common.h util.h wutil.h exec.h proc.h io.h
+intern.o: config.h fallback.h util.h wutil.h common.h intern.h
+io.o: config.h fallback.h util.h wutil.h exec.h proc.h io.h common.h
 io.o: translate.h halloc.h
-key_reader.o: fallback.h common.h util.h input_common.h
-kill.o: signal.h config.h fallback.h common.h util.h wutil.h kill.h proc.h
-kill.o: io.h sanity.h env.h exec.h parser.h event.h
-main.o: config.h signal.h fallback.h common.h util.h reader.h builtin.h
+key_reader.o: config.h fallback.h input_common.h
+kill.o: signal.h config.h fallback.h util.h wutil.h kill.h proc.h io.h
+kill.o: sanity.h common.h env.h exec.h parser.h event.h halloc.h
+main.o: config.h signal.h fallback.h util.h common.h reader.h builtin.h
 main.o: function.h complete.h wutil.h env.h sanity.h proc.h io.h parser.h
 main.o: event.h expand.h intern.h exec.h output.h translate.h halloc_util.h
 main.o: history.h
-mimedb.o: config.h xdgmime.h fallback.h common.h util.h
-output.o: config.h signal.h fallback.h common.h util.h wutil.h expand.h
+mimedb.o: config.h xdgmime.h fallback.h util.h
+output.o: config.h signal.h fallback.h util.h wutil.h expand.h common.h
 output.o: output.h halloc_util.h highlight.h
-parser.o: signal.h config.h fallback.h common.h util.h wutil.h proc.h io.h
+parser.o: signal.h config.h fallback.h util.h common.h wutil.h proc.h io.h
 parser.o: parser.h event.h tokenizer.h exec.h wildcard.h function.h builtin.h
-parser.o: builtin_help.h env.h expand.h reader.h sanity.h env_universal.h
+parser.o: env.h expand.h reader.h sanity.h env_universal.h
 parser.o: env_universal_common.h translate.h intern.h parse_util.h halloc.h
 parser.o: halloc_util.h
-parse_util.o: config.h fallback.h common.h util.h wutil.h tokenizer.h
+parse_util.o: config.h fallback.h util.h wutil.h common.h tokenizer.h
 parse_util.o: parse_util.h expand.h intern.h exec.h proc.h io.h env.h
 parse_util.o: wildcard.h halloc_util.h
-proc.o: config.h signal.h fallback.h common.h util.h wutil.h proc.h io.h
+proc.o: config.h signal.h fallback.h util.h wutil.h proc.h io.h common.h
 proc.o: reader.h sanity.h env.h parser.h event.h translate.h halloc.h
 proc.o: halloc_util.h output.h
-reader.o: config.h signal.h fallback.h common.h util.h wutil.h highlight.h
-reader.o: reader.h proc.h io.h parser.h event.h complete.h history.h sanity.h
+reader.o: config.h signal.h fallback.h util.h wutil.h highlight.h reader.h
+reader.o: proc.h io.h parser.h event.h complete.h history.h common.h sanity.h
 reader.o: env.h exec.h expand.h tokenizer.h kill.h input_common.h input.h
 reader.o: function.h output.h translate.h parse_util.h
-refcount.o: config.h fallback.h common.h util.h wutil.h refcount.h
-sanity.o: signal.h config.h fallback.h common.h util.h sanity.h proc.h io.h
+sanity.o: signal.h config.h fallback.h util.h common.h sanity.h proc.h io.h
 sanity.o: history.h reader.h kill.h wutil.h translate.h
 set_color.o: config.h
 signal.o: config.h signal.h common.h util.h fallback.h wutil.h event.h
 signal.o: reader.h proc.h io.h translate.h
-tokenizer.o: config.h fallback.h common.h util.h wutil.h tokenizer.h
+tokenizer.o: config.h fallback.h util.h wutil.h tokenizer.h common.h
 tokenizer.o: wildcard.h translate.h
 translate.o: config.h common.h util.h fallback.h halloc_util.h
-util.o: config.h fallback.h common.h util.h wutil.h
-wgetopt.o: config.h wgetopt.h wutil.h fallback.h common.h util.h translate.h
-wildcard.o: config.h fallback.h common.h util.h wutil.h complete.h wildcard.h
+util.o: config.h fallback.h util.h common.h wutil.h
+wgetopt.o: config.h wgetopt.h wutil.h fallback.h translate.h
+wildcard.o: config.h fallback.h util.h wutil.h complete.h common.h wildcard.h
 wildcard.o: reader.h expand.h translate.h
-wutil.o: config.h fallback.h common.h util.h wutil.h
+wutil.o: config.h fallback.h util.h common.h wutil.h
 xdgmimealias.o: xdgmimealias.h xdgmime.h xdgmimeint.h
 xdgmime.o: xdgmime.h xdgmimeint.h xdgmimeglob.h xdgmimemagic.h xdgmimealias.h
 xdgmime.o: xdgmimeparent.h
diff --git a/builtin.c b/builtin.c
index e896ac916..e1997b20a 100644
--- a/builtin.c
+++ b/builtin.c
@@ -54,7 +54,6 @@
 #include "wgetopt.h"
 #include "sanity.h"
 #include "tokenizer.h"
-#include "builtin_help.h"
 #include "wildcard.h"
 #include "input_common.h"
 #include "input.h"
@@ -67,6 +66,13 @@
 #include "parse_util.h"
 #include "expand.h"
 
+#include "builtin_help.c"
+#include "builtin_set.c"
+#include "builtin_commandline.c"
+#include "builtin_complete.c"
+#include "builtin_ulimit.c"
+#include "builtin_jobs.c"
+
 /**
    The default prompt for the read command
 */
@@ -2942,8 +2948,6 @@ void builtin_init()
 		hash_put( &builtin, builtin_data[i].name, builtin_data[i].func );
 		intern_static( builtin_data[i].name );
 	}
-	
-	builtin_help_init();
 }
 
 void builtin_destroy()
@@ -2957,7 +2961,6 @@ void builtin_destroy()
 
 	al_destroy( &io_stack );
 	hash_destroy( &builtin );
-	builtin_help_destroy();
 }
 
 int builtin_exists( wchar_t *cmd )
diff --git a/builtin.h b/builtin.h
index 95d837670..511a046b2 100644
--- a/builtin.h
+++ b/builtin.h
@@ -150,36 +150,6 @@ int builtin_count_args( wchar_t **argv );
 void builtin_print_help( wchar_t *cmd, string_buffer_t *b );
 
 
-/**
-   The set builtin, used for setting variables. Defined in
-   builtin_set.c.
-*/
-int builtin_set(wchar_t **argv);
-
-/**
-   The commandline builtin, used for setting and getting the contents
-   of the commandline. Defined in builtin_commandline.c.
-*/
-int builtin_commandline(wchar_t **argv);
-
-/**
-   The ulimit builtin, used for setting resource limits. Defined in
-   builtin_ulimit.c.
-*/
-int builtin_ulimit(wchar_t **argv);
-
-/**
-   The complete builtin. Used for specifying programmable
-   tab-completions. Calls the functions in complete.c for any heavy
-   lifting. Defined in builtin_complete.c
-*/
-int builtin_complete(wchar_t **argv);
-
-/**
-   The jobs builtin. Used fopr printing running jobs. Defined in builtin_jobs.c.
-*/
-int builtin_jobs(wchar_t **argv);
-
 const wchar_t *builtin_complete_get_temporary_buffer();
 
 /** 
@@ -189,4 +159,13 @@ const wchar_t *builtin_complete_get_temporary_buffer();
 */
 void builtin_wperror( const wchar_t *s);
 
+/**
+   Return the help text for the specified builtin command. Use
+   non-wide characters since wide characters have some issues with
+   string formating escape sequences sometimes.
+
+   \param cmd The command for which to obtain help text
+*/
+char *builtin_help_get( wchar_t *cmd );
+
 #endif
diff --git a/builtin_commandline.c b/builtin_commandline.c
index 3d0f77e0b..19e604715 100644
--- a/builtin_commandline.c
+++ b/builtin_commandline.c
@@ -195,7 +195,7 @@ static void write_part( const wchar_t *begin,
    The commandline builtin. It is used for specifying a new value for
    the commandline.
 */
-int builtin_commandline( wchar_t **argv )
+static int builtin_commandline( wchar_t **argv )
 {
 
 	int buffer_part=0;
diff --git a/builtin_complete.c b/builtin_complete.c
index 1519f5db2..e93f9cde3 100644
--- a/builtin_complete.c
+++ b/builtin_complete.c
@@ -249,7 +249,12 @@ const wchar_t *builtin_complete_get_temporary_buffer()
 	return temporary_buffer;
 }
 
-int builtin_complete( wchar_t **argv )
+/**
+   The complete builtin. Used for specifying programmable
+   tab-completions. Calls the functions in complete.c for any heavy
+   lifting. Defined in builtin_complete.c
+*/
+static int builtin_complete( wchar_t **argv )
 {
 	int res=0;
 	int argc=0;
diff --git a/builtin_help.h b/builtin_help.h
deleted file mode 100644
index c831b3e41..000000000
--- a/builtin_help.h
+++ /dev/null
@@ -1,32 +0,0 @@
-/** \file builtin_help.h 
-
-    Prototypes for functions for printing usage information of builtin commands. The
-	corresponding .c file is automatically generated by combining the
-	builtin_help.hdr file with doxygen output.
-*/
-
-#ifndef FISH_BUILTIN_HELP_H
-#define FISH_BUILTIN_HELP_H
-
-#include <wchar.h>
-
-/**
-   Return the help text for the specified builtin command. Use
-   non-wide characters since wide characters have some issues with
-   string formating escape sequences sometimes.
-
-   \param cmd The command for which to obtain help text
-*/
-char *builtin_help_get( wchar_t *cmd );
-
-/**
-   Initialize builtin help data
-*/
-void builtin_help_init();
-
-/**
-   Destory builtin help data
-*/
-void builtin_help_destroy();
-
-#endif
diff --git a/builtin_help.hdr b/builtin_help.hdr
index 7507fae29..c2671a5f3 100644
--- a/builtin_help.hdr
+++ b/builtin_help.hdr
@@ -14,24 +14,28 @@
 #include "config.h"
 #include "util.h"
 #include "common.h"
-#include "builtin_help.h"
+#include "halloc_util.h"
+
+static int is_help_init=0;
 
 /**
 	Hashtable storing the help text
 */
 static hash_table_t tbl;
 
+static void builtin_help_init();
+
 char *builtin_help_get( wchar_t *cmd )
 {
+	if( !is_help_init )
+	{
+		builtin_help_init();
+	}
 	return (char *)hash_get( &tbl, (void *)cmd );
 }
 
-void builtin_help_destroy()
-{
-	hash_destroy( &tbl );
-}
-
-
-void builtin_help_init()
+static void builtin_help_init()
 {
+	is_help_init = 1;
+	halloc_register_function( global_context, (void (*)(void *))&hash_destroy, &tbl );
 	hash_init( &tbl, &hash_wcs_func, &hash_wcs_cmp );
diff --git a/builtin_jobs.c b/builtin_jobs.c
index 0a3f2d707..a527fdf0e 100644
--- a/builtin_jobs.c
+++ b/builtin_jobs.c
@@ -158,7 +158,10 @@ static void builtin_jobs_print( job_t *j, int mode, int header )
 
 
 
-int builtin_jobs( wchar_t **argv )
+/**
+   The jobs builtin. Used fopr printing running jobs. Defined in builtin_jobs.c.
+*/
+static int builtin_jobs( wchar_t **argv )
 {
 	int argc=0;
 	int found=0;
diff --git a/builtin_set.c b/builtin_set.c
index 1e3e42b15..6841aeb48 100644
--- a/builtin_set.c
+++ b/builtin_set.c
@@ -381,7 +381,7 @@ static void print_variables(int include_values, int esc, int scope)
    The set builtin. Creates, updates and erases environment variables
    and environemnt variable arrays.
 */
-int builtin_set( wchar_t **argv ) 
+static int builtin_set( wchar_t **argv ) 
 {
 	
 	/**
diff --git a/builtin_ulimit.c b/builtin_ulimit.c
index d03521939..6b8c7b7ee 100644
--- a/builtin_ulimit.c
+++ b/builtin_ulimit.c
@@ -257,7 +257,11 @@ static int set_all( int hard, int soft, rlim_t value )
 	return res;
 }
 
-int builtin_ulimit( wchar_t ** argv )
+/**
+   The ulimit builtin, used for setting resource limits. Defined in
+   builtin_ulimit.c.
+*/
+static int builtin_ulimit( wchar_t ** argv )
 {
 	int hard=0;
 	int soft=0;
diff --git a/common.c b/common.c
index f9bfdca84..9475fd64c 100644
--- a/common.c
+++ b/common.c
@@ -61,6 +61,11 @@ parts of fish.
 #include "wildcard.h"
 #include "parser.h"
 
+#include "util.c"
+#include "halloc.c"
+#include "halloc_util.c"
+#include "fallback.c"
+
 /**
    The number of milliseconds to wait between polls when attempting to acquire 
    a lockfile
diff --git a/parser.c b/parser.c
index b717bda2f..daedbdad5 100644
--- a/parser.c
+++ b/parser.c
@@ -31,7 +31,6 @@ The fish parser. Contains functions for parsing code.
 #include "wildcard.h"
 #include "function.h"
 #include "builtin.h"
-#include "builtin_help.h"
 #include "env.h"
 #include "expand.h"
 #include "reader.h"
@@ -256,11 +255,14 @@ The fish parser. Contains functions for parsing code.
    Size of the error string buffer
 */
 #define ERR_STR_SZ 1024
+
 /** Last error code */
-int error_code;
+static int error_code;
 
 event_block_t *global_event_block=0;
 
+io_data_t *block_io;
+
 /** Position of last error */
 
 static int err_pos;
@@ -288,8 +290,6 @@ static array_list_t *forbidden_function;
 */
 static int job_start_pos;
 
-io_data_t *block_io;
-
 /**
    List of all profiling data
 */
diff --git a/parser.h b/parser.h
index 604289360..e82a6e7f9 100644
--- a/parser.h
+++ b/parser.h
@@ -191,10 +191,6 @@ extern block_t *current_block;
 /** Global event blocks */
 extern event_block_t *global_event_block;
 
-
-/** The current error code */
-extern int error_code;
-
 /**
    Current block level io redirections 
 */
diff --git a/proc.c b/proc.c
index b3519e2df..56c43ebd0 100644
--- a/proc.c
+++ b/proc.c
@@ -171,6 +171,7 @@ void proc_destroy()
 
 void proc_set_last_status( int s )
 {
+
 	last_status = s;
 	//	fwprintf( stderr, L"Set last status to %d\n", s );
 }