As of today using Strawberry Perl 184.108.40.206 (64bit), Perl doesn't automatically adapt chomp at all to the platform nor converts automatically the carriage return from files that are read.
For me, it always just remove \n, and that's all.
My solution: either change the special var as suggested above, or use your own chomp with a substitution regexp: s/(\n|\r)//g
Or of course, change the carriage return of all your files.
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