Well, with respect to maintainability, I would think that File::Find would be much easier to maintain, once you understand how it works.

As for your code, the problem is the line

my @files = readdir(DIR) || die "Unable to read $workdir: $!\n";
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The || operator has a higher precedence than the assignment, which means the readdir() gets evaluated in a scalar context; i.e., it returns only one directory entry. Try the or operator, for the effect you're looking for:

my @files = readdir(DIR) or die "Unable to read $workdir: $!\n";
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(Now, if you had been using File::Find, you wouldn't have had to figure this out ;-) ...)