If you are absolutely sure that they are text files, ... something like the following could be used to normalize everything to match your current system's line endings.
Assume the content of the file is in $file:
$file =~ s/(\x0d?\x0a|\x0d)/\n/smg;
Now when you write the string to disk, the line endings will be consistent.
It's important to do the alternation in the correct order, otherwise you can get a surprising result. If you don't have to worry about old Macs, you can get away with:
$file =~ s/\x0d?\x0a/\n/smg;
Make certain you don;t do this to non-text files, the results are not recoverable.
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