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foreach my $file (@files) {
    next if $file =~ m#/CVS/#;
...
    $file =~ s#^\./##;
    push(@noCvsDirs, $file);
}

my $full_file = ($dir eq '.' ? $file : "$dir/$file");

use File::Spec ();

...
      File::Spec->catfile($dir, $file)
   )
);