Actually, subversion can be used for this task. Just store the permissions as properties. This also allows you to store ACLs, have version control (and check-in notes) on the permission changes, etc, etc...

A useful resource would probably be the various API bindings. From this you can use the check-in/check-out hooks to do something like:

    use SVN::Client;

    my $svn = new SVN::Client();
    $svn->propset("acl:joe", "rw", $target, 0, 0);

    # Where $target is the local (checked out) copy
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NB. The SVN perl bindings are NOT in CPAN. You need to get them along with subversion. (Discussion)