diff -Nurd -x'*~' flag-sort-0.5.orig/flag-sort flag-sort-0.5/flag-sort
--- flag-sort-0.5.orig/flag-sort	1969-12-31 19:00:00.000000000 -0500
+++ flag-sort-0.5/flag-sort	2012-12-08 15:55:45.000000000 -0500
@@ -0,0 +1,138 @@
+#!/usr/bin/perl
+# -*- mode: Perl; tab-width: 4; -*-
+
+# A dirty hack by Daniel Macks
+
+use warnings;
+use strict;
+
+# all flags for a listed prefix are grouped together before the next prefix
+my @prefix_order = (
+	'@PREFIX@/opt',
+	'@PREFIX@/lib',
+	'@PREFIX@/include',
+	'/opt/X11/lib',
+	'/opt/X11/include',
+	'/usr/X11/lib',
+	'/usr/X11/include',
+	'/usr/X11R6/lib',
+	'/usr/X11R6/include',
+	'/usr/lib',
+	'/usr/include',
+	'/usr/local/lib',
+	'/usr/local/include'
+);
+
+# track the following flags (in this order)
+my @flag_order = (
+	'-I',
+	'-L',
+);
+my %flag_queues = ();	 # $flag => \@paths_for_flag
+my @other_queue = ();	 # things not fitting into any of %flag_queues
+
+my $verbose = 0;
+my $relative_first = 0;
+
+while ($ARGV[0] =~ /^-(v|r)/) {
+	if ($ARGV[0] eq '-v') {
+		$verbose = 1;
+		shift;
+	} elsif ($ARGV[0] eq '-r') {
+		$relative_first = 1;
+		shift;
+	}
+}
+
+if (!@ARGV) {
+	warn "Usage: $0 [-v] [-r] cmd [flags for cmd]\n";
+	warn "  resort [flags for cmd] and call cmd with them\n";
+	warn "  -r causes sort to put relative paths before absolute paths\n";
+	warn "  -v causes display of some diagnostics on STDOUT\n";
+	exit 1;
+}
+
+# full paths should be after relative paths
+sub bypath {
+	my ($a_path) = $a =~ /^-(?:I|L)(.*)$/;
+	my ($b_path) = $b =~ /^-(?:I|L)(.*)$/;
+
+	#print "a_path = $a_path\n";
+	#print "b_path = $b_path\n";
+
+	if (not defined $a_path or not defined $b_path) {
+		return 0;
+	}
+
+	if ($a_path =~ /^\//) {
+		if ($b_path =~ /^\//) {
+			return 0;
+		} else {
+			return 1;
+		}
+	} else {
+		if ($b_path =~ /^[\/]/) {
+			return -1;
+		} else {
+			return 0;
+		}
+	}
+
+	return 0;
+}
+
+# what we will launch after organizing the flags
+my @subcmd = ();
+
+# separate the args according to flag
+while (@ARGV) {
+	my $arg = shift;
+	my($flag) = grep { $arg =~ s/^$_// } @flag_order;
+	if (defined $flag) {
+		# parsed off a known flag
+		push @{$flag_queues{$flag}}, $arg;
+	} else {
+		# unknown flag
+		push @other_queue, $arg;
+	}
+}
+
+#assume totally unknown flags and args are most important
+push @subcmd, @other_queue;
+
+# sort all paths for each flag
+foreach my $flag (@flag_order) {
+	next unless defined $flag_queues{$flag};
+	my @path_list = @{$flag_queues{$flag}};
+	#warn "$0: $flag: @path_list\n";
+
+	# first separate the paths according to prefix
+	my %sorted_paths;			# $prefix => \@sorted_dirs_for_prefix
+	my @other_paths;			# paths not under any of %sorted_paths
+	foreach my $path (@{$flag_queues{$flag}}) {
+		my($prefix) = grep { $path =~ /^$_(\/|\z)/ } @prefix_order;
+		if (defined $prefix) {
+			# $path is $prefix or a subdir of it
+			push @{$sorted_paths{$prefix}}, $path;
+		} else {
+			# unknown prefix
+			push @other_paths, $path;
+		}
+	}
+
+	# now reconstruct list of paths according to prefix priority
+	@path_list = @other_paths;  # assume unknowns are "very important"
+	foreach my $prefix (@prefix_order) {
+		push(@path_list, @{$sorted_paths{$prefix}}) if exists $sorted_paths{$prefix};
+	}
+	#warn "$0: now $flag: @path_list\n";
+	if ($relative_first) {
+		push @subcmd, sort bypath map "$flag$_", @path_list;
+	} else {
+		push @subcmd, map "$flag$_", @path_list;
+	}
+}
+
+print "$0: @subcmd\n" if $verbose;
+exec {$subcmd[0]} @subcmd or die "Could not exec $subcmd[0]: $!\n";
+