opendir PLUGINS, "conf/plugins" or die "unable to opendir ./conf/plugins\n";
while (my $pluginfile = readdir(PLUGINS) ) {
    my $localfile = Bio::Root::IO->catfile('conf/plugins',$pluginfile);
    if (-f $localfile) {
        my $installfile = Bio::Root::IO->catfile($plugindir, $pluginfile);
        chmod (0666, $installfile);
        copy($localfile, $installfile)
            or die "$localfile unable to copy to $installfile : $!\n";
        chmod (0444, $installfile);
    }
}
closedir PLUGINS;