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use strict;
use warnings;
...
       my ($fname, $fext) = split(' ',$line);
       $duplicates{$fname}{$fext}++;
}

/foo/bar/baz/123 aaa
/foo/bar/baz/123 aab
/foo/bar/baz/123 aac
/foo/bar/baz/124 aaa
/foo/bar/baz/124 aab