The reason for the problem is that the filetests are going against the file names directly. So if you are listing files in directory /foo while you are in /bar, you are looking at whether /bar/baz is an old file when what you really wanted to know is whether /foo/baz is an old file.

You have posted one workaround. The other is:

my $logdir = "/whatdir/";

opendir(LOGDIR, $logdir) or die "Can't open '$logdir': $!\n";
foreach my $file (
  grep {-f && (-M > 5)} map "$logdir$_", readdir(LOGDIR)
) {
    unlink $file;
}
closedir(LOGDIR);
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