For POSIX systems, the first two values in the list returned by Perl's stat builtin provide a solution. These are the "device" and "inode" numbers for the file and, taken as a pair, uniquely identify a file.

# return true if both names are for the same file
sub check_same_file_under_posix {
    my ($file_a, $file_b) = @_;

    my ($dev_a, $ino_a, @other_a) = stat($file_a);
    my ($dev_b, $ino_b, @other_b) = stat($file_b);

    if (($dev_a == $dev_b) && ($ino_a == $ino_b)) { return 1 }
    else { return 0 }
}
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