In general, if you're using for() to iterate over a list that you're modifying within the loop: that's a danger sign. Something will get messed up sooner or later, and be tough to track down. Instead, try this simple structure instead of the for:

    while(@dirs) {
         my $dir=shift @dirs;

         # Rest of loop here
    }
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This way you can throw stuff anywhere you want to in @dirs, and it'll all get processed eventually. By changing the push to an unshift, you'll get a depth-first search instead of breadth-first. Nifty, eh?

You do have a couple of other small bugs, which other posters have pointed out.