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Hello,I've hit problems trying to apply a dos-like patch to a unix-like file, and vice-versa, but not what you describe. Also, problems with line endings tend to go all-or-nothing: either all hunks fail (all line endings differ), or all succeed in the absence of other conflicts.
using Cygwin patch.exe in a batch file I ran into the problem that patch failed for some reason ("hunk 1 out of 3 hunks failed"):
Investigating this issue I found that inserting "unix2dos my.patch" before applying the patch was my friend! Being paranoid I tried "dos2unix my.patch" before applying the patch - and it was my friend too!
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