Digest::MD5 is not necessary. The script should still execute correctly if it's not present. There's code to use Digest::MD5 if it's there, otherwise a different method of file comparison is used.
Perl is complaining that one of the two variables used in a string comparison (ne = string not-equals) has no value (undefined).
So, either the data being read from the file passed to the routine is null or the $$content value it's comparing against is null.
This requires more debug information than we have available. Knowing the values of $file and $content passed to the subroutine would be helpful.
Then again, installing Digest::MD5 runs a different chunk of code, so it may fix the error by avoidance!