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use strict;
use Digest::MD5;
...
        print qq{\t\t}, join( qq{\n\t\t}, @{$files{$k}} ), qq{\n};
    }
}

$ ./compare-test.pl .
The following entries appear to be duplicates, and warrant closer 
...
        Checksum: 3ef60d5a2fa552f395e154bb5418893c
                ./file-5.txt
                ./file5.txt