diff --git a/Makefile.in b/Makefile.in
index 0e1597efd..1bbabf9c7 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -47,7 +47,6 @@ datadir = @datadir@
 bindir = @bindir@
 mandir = @mandir@
 sysconfdir = @sysconfdir@
-fishinputfile = @fishinputfile@
 docdir = @docdir@
 
 #etc files to install
@@ -184,7 +183,7 @@ TRANSLATIONS_SRC := $(wildcard po/*.po)
 TRANSLATIONS := $(TRANSLATIONS_SRC:.po=.gmo)
 
 #Make everything needed for installing fish
-all: $(PROGRAMS) user_doc
+all: $(PROGRAMS) user_doc etc/fish share/fish
 	@echo fish has now been built. 
 	@echo Use \'make install\' to install fish.
 .PHONY: all
@@ -250,6 +249,10 @@ doc.h:$(BUILTIN_DOC_SRC) $(CMD_DOC_SRC) doc_src/doc.hdr
 	cat $*.txt >>$@; 
 	echo "*/" >>$@
 
+%: %.in Makefile
+	sed <$@.in >$@ -e "s,@sysconfdir\@,$(sysconfdir)," -e "s,@datadir\@,$(datadir)," -e "s,@docdir\@,$(docdir)," -e "s|@configure_input\@|$@, generated from $@.in by the Makefile. DO NOT MANUALLY EDIT THIS FILE!|" 
+#-e "s,@\@,$()," 
+
 # Compile translation file
 %.gmo:
 	if test $(HAVE_GETTEXT) = 1; then \
@@ -511,7 +514,7 @@ set_color: set_color.o doc_src/set_color.o common.o
 
 # Test program for the tokenizer library
 tokenizer_test: tokenizer.c tokenizer.h wutil.o common.o
-	$(CC) ${CFLAGS} tokenizer.c wutil.o common.o -D TOKENIZER_TEST $(LDFLAGS) -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 common.o env_universal.o env_universal_common.o wutil.o
diff --git a/configure.ac b/configure.ac
index 205d1bfe9..16efd236c 100644
--- a/configure.ac
+++ b/configure.ac
@@ -230,12 +230,11 @@ AC_SUBST( DATADIR, ["$(eval echo $datadir)"] )
 AC_ARG_VAR( [docdir], [Documentation direcotry] )
 
 if test -z $docdir; then
-   AC_SUBST(docdir,[$datadir/doc/fish])
+   AC_SUBST(docdir, [$datadir/doc/fish] )
+else
+   AC_SUBST(docdir, [$docdir])
 fi
 
-AC_DEFINE_UNQUOTED( DOCDIR, [L"$(eval echo $docdir)"], [Documentation directory] )
-
-
 # Set up locale directory. This is where the .po files will be
 # installed.
 AC_DEFINE_UNQUOTED( [LOCALEDIR], "$(eval echo $datadir)/locale", [Locale directory])
@@ -348,7 +347,7 @@ case $target_os in
 esac
 
 # Tell the world what we know
-AC_CONFIG_FILES([Makefile fish.spec doc_src/fish.1 doc_src/Doxyfile etc/fish etc/fish_interactive.fish share/fish seq])
+AC_CONFIG_FILES([Makefile fish.spec doc_src/fish.1 doc_src/Doxyfile etc/fish_interactive.fish seq])
 AC_OUTPUT
 
 echo "fish is now configured."
diff --git a/etc/fish.in b/etc/fish.in
index fd04a5874..5b5c72edf 100644
--- a/etc/fish.in
+++ b/etc/fish.in
@@ -7,8 +7,8 @@
 # Set default search paths for completions and shellscript functions
 #
 
-set -g fish_function_path ~/.fish.d/functions    @SYSCONFDIR@/fish.d/functions    @DATADIR@/fish/functions 
-set -g fish_complete_path ~/.fish.d/completions  @SYSCONFDIR@/fish.d/completions  @DATADIR@/fish/completions 
+set -g fish_function_path ~/.fish.d/functions    @sysconfdir@/fish.d/functions    @datadir@/fish/functions 
+set -g fish_complete_path ~/.fish.d/completions  @sysconfdir@/fish.d/completions  @datadir@/fish/completions 
 
 #
 # Set default field separators
diff --git a/main.c b/main.c
index 47231dc53..458c6841f 100644
--- a/main.c
+++ b/main.c
@@ -81,8 +81,6 @@ static int read_init()
 		return 0;
 	}
 
-	env_set( L"__fish_help_dir", DOCDIR, 0);	
-
 	eval( L"builtin cd " DATADIR L"/fish 2>/dev/null; and . fish 2>/dev/null", 0, TOP );
 	eval( L"builtin cd " SYSCONFDIR L" 2>/dev/null; and . fish 2>/dev/null", 0, TOP );
 	eval( L"builtin cd 2>/dev/null; and . .fish 2>/dev/null", 0, TOP );
diff --git a/share/fish.in b/share/fish.in
index a7e6e1dd0..226a5a24a 100644
--- a/share/fish.in
+++ b/share/fish.in
@@ -3,12 +3,14 @@
 # common helper functions for the command completions. All actual
 # completions are located in the completions subdirectory.
 #
+# @configure_input@
 
-#
-# Assign a temporary value here for performance reasons. The real value should be set in /etc/fish.
-#
+# Assign a temporary value here for performance reasons. The real
+# value should be set in /etc/fish.
+
+set -g fish_function_path @datadir@/functions/
+set __fish_help_dir @docdir@
 
-set -g fish_function_path $PWD/functions/
 
 #
 # Make sure there are no invalid entries in the PATH