diff -ur gpt.orig/packaging_tools/perl/GPT/Filelist.pm gpt/packaging_tools/perl/GPT/Filelist.pm
--- gpt.orig/packaging_tools/perl/GPT/Filelist.pm	2008-12-15 08:33:05.000000000 +0100
+++ gpt/packaging_tools/perl/GPT/Filelist.pm	2008-12-15 09:10:15.000000000 +0100
@@ -115,7 +115,9 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'name'} =~ /\.h$/ and $_->{'dir'} =~ m!include/$f!) {
+    if ($_->{'name'} =~ /\.h$/
+	and ($_->{'dir'} =~ m!include/$f! or
+	     $_->{'dir'} =~ m!lib(64)?(/.*)?/include!)) {
       push @newlist, $_;
     }
   }
@@ -127,7 +129,9 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'name'} =~ /\.h$/ and $_->{'dir'} !~ m!include/$f!) {
+    if ($_->{'name'} =~ /\.h$/
+	and ($_->{'dir'} !~ m!include/$f! and
+	     $_->{'dir'} !~ m!lib(64)?(/.*)?/include!)) {
       push @newlist, $_;
     }
   }
@@ -151,7 +155,7 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'dir'} =~ m!^/setup/!) {
+    if ($_->{'dir'} =~ m!(?:/|^)setup(?:/|$)!) {
       push @newlist, $_;
     }
   }
@@ -163,7 +167,11 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'name'} =~ /\.a$/ and $_->{'dir'} =~ m!lib/*$!) {
+    if ( ( $_->{'name'} =~ m!\.a$!
+           or $_->{'name'} =~ m!^[^.]*\.so$!
+           or $_->{'name'} =~ m!^[^.]*\.sl$!
+           or $_->{'name'} =~ m!^[^.]*\.dylib$! )
+         and $_->{'name'} =~ m!^lib!) {
       push @newlist, $_;
     }
   }
@@ -175,9 +183,9 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ( ( $_->{'name'} =~ m!\.so! 
-           or $_->{'name'} =~ m!\.sl!
-           or $_->{'name'} =~ m!\.dylib! ) 
+    if ( ( $_->{'name'} =~ m!(?:\.so\.|\.[^.]+\.so)!
+           or $_->{'name'} =~ m!(?:\.sl\.|\.[^.]+\.sl)!
+           or $_->{'name'} =~ m!(?:\.dylib\.|\.[^.]+\.dylib)! )
          and $_->{'name'} =~ m!^lib!) {
       push @newlist, $_;
     }
@@ -214,7 +222,7 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'dir'} =~ m!(?:/|^)(?:share/doc|man)(?:/|$)!) {
+    if ($_->{'dir'} =~ m!(?:/|^)(?:share/doc|man|share/man)(?:/|$)!) {
       push @newlist, $_;
     }
   }
@@ -226,7 +234,7 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'dir'} !~ m!(?:/|^)(?:share/doc|man|s?bin|libexec|include|lib|setup|share/globus/packages)(?:/|$)!) {
+    if ($_->{'dir'} !~ m!(?:/|^)(?:share/doc|man|share/man|s?bin|libexec|include|lib(64)?|setup|share/globus/packages)(?:/|$)!) {
       push @newlist, $_;
     }
   }
diff -ur gpt.orig/packaging_tools/perl/GPT/FilelistSort.pm gpt/packaging_tools/perl/GPT/FilelistSort.pm
--- gpt.orig/packaging_tools/perl/GPT/FilelistSort.pm	2008-12-15 08:33:05.000000000 +0100
+++ gpt/packaging_tools/perl/GPT/FilelistSort.pm	2008-12-15 09:11:00.000000000 +0100
@@ -112,7 +112,9 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'name'} =~ /\.h$/ and $_->{'dir'} =~ m!include/$f!) {
+    if ($_->{'name'} =~ /\.h$/
+	and ($_->{'dir'} =~ m!include/$f! or
+	     $_->{'dir'} =~ m!lib(64)?(/.*)?/include!)) {
       push @newlist, $_;
     }
   }
@@ -124,7 +126,9 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'name'} =~ /\.h$/ and $_->{'dir'} !~ m!include/$f!) {
+    if ($_->{'name'} =~ /\.h$/
+	and ($_->{'dir'} !~ m!include/$f! and
+	     $_->{'dir'} !~ m!lib(64)?(/.*)?/include!)) {
       push @newlist, $_;
     }
   }
@@ -148,7 +152,7 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'dir'} =~ m!^/setup/!) {
+    if ($_->{'dir'} =~ m!(?:/|^)setup(?:/|$)!) {
       push @newlist, $_;
     }
   }
@@ -160,9 +164,11 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    # Changed to allow for lib/subdir/lib.a while still allowing
-    # lib/lib.a, where apparently the dir is just lib, not lib/
-    if ($_->{'name'} =~ /\.a$/ and $_->{'dir'} =~ m!lib$|lib/!) {
+    if ( ( $_->{'name'} =~ m!\.a$!
+           or $_->{'name'} =~ m!^[^.]*\.so$!
+           or $_->{'name'} =~ m!^[^.]*\.sl$!
+           or $_->{'name'} =~ m!^[^.]*\.dylib$! )
+         and $_->{'name'} =~ m!^lib!) {
       push @newlist, $_;
     }
   }
@@ -174,9 +180,9 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ( ( $_->{'name'} =~ m!\.so! 
-           or $_->{'name'} =~ m!\.sl! 
-           or $_->{'name'} =~ m!\.dylib! ) 
+    if ( ( $_->{'name'} =~ m!(?:\.so\.|\.[^.]+\.so)!
+           or $_->{'name'} =~ m!(?:\.sl\.|\.[^.]+\.sl)!
+           or $_->{'name'} =~ m!(?:\.dylib\.|\.[^.]+\.dylib)! )
          and $_->{'name'} =~ m!^lib!) {
       push @newlist, $_;
     }
@@ -213,7 +219,7 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'dir'} =~ m!(?:/|^)(?:share/doc|man)(?:/|$)!) {
+    if ($_->{'dir'} =~ m!(?:/|^)(?:share/doc|man|share/man)(?:/|$)!) {
       push @newlist, $_;
     }
   }
@@ -225,7 +231,7 @@
   my $list = $self->{'list'};
   my @newlist;
   for (@{$list}) {
-    if ($_->{'dir'} !~ m!(?:/|^)(?:share/doc|man|s?bin|libexec|include|lib|setup|share/globus/packages)(?:/|$)!) {
+    if ($_->{'dir'} !~ m!(?:/|^)(?:share/doc|man|share/man|s?bin|libexec|include|lib(64)?|setup|share/globus/packages)(?:/|$)!) {
       push @newlist, $_;
     }
   }
diff -ur gpt.orig/packaging_tools/perl/GPT/MyFilelists.pm gpt/packaging_tools/perl/GPT/MyFilelists.pm
--- gpt.orig/packaging_tools/perl/GPT/MyFilelists.pm	2006-01-11 17:10:11.000000000 +0100
+++ gpt/packaging_tools/perl/GPT/MyFilelists.pm	2008-12-15 09:07:13.000000000 +0100
@@ -68,6 +68,12 @@
   push @$result, @$list;
   $me->{'filelist'}->reset();
 
+  $me->{'filelist'}->flavored_files() if defined $me->{'mangling'};
+  $me->{'filelist'}->extract_libtool_libs();
+  $list = $me->{'filelist'}->get_list();
+  push @$result, @$list;
+  $me->{'filelist'}->reset();
+
   $me->{'filelist'}->extract_perl_modules();
   $list = $me->{'filelist'}->get_list();
   push @$result, @$list;
@@ -85,12 +91,6 @@
   push @$result, @$list;
   $me->{'filelist'}->reset();
 
-  $me->{'filelist'}->flavored_files() if defined $me->{'mangling'};
-  $me->{'filelist'}->extract_libtool_libs();
-  $list = $me->{'filelist'}->get_list();
-  push @$result, @$list;
-  $me->{'filelist'}->reset();
-
   $me->{'filelist'}->flavored_headers() if defined $me->{'mangling'};
   $me->{'filelist'}->add_package_metadata_files('dev');
   $list = $me->{'filelist'}->get_list();