Are you saying that the dot (.) directory somehow makes it past the grep {-f} filter in the OP's code?

I guess I was without realizing it. Obviously, that's not true and my explanation is wrong. Take two:

$ext{$1} += (m/([^.]+)$/);
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means something close to

$ext{$1} = $ext{$1} + (m/([^.]+)$/);
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Well, actually more like the following, but it doesn't matter for this discussion:

alias $temp = $ext{$1};
$temp = $temp + (m/([^.]+)$/);
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Either way, you are relying on Perl evaluating the RHS of the "+=" operator before its LHS, and that's not how Perl operates. In fact, Perl doesn't document how it operates in this circumstance, and that's the reason it's generally a no-no to change and use the same variable in the same expression.

Even though my earlier explanation was wrong, the solutions I posted still avoid the problem.

Update: Improved phrasing by inlining footnotes.