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The diff command, even using git option, includes path prefixes commonly used on DCS:
--- a/file.ext
+++ b/file.ext
So applying such patches you should need to using -p1 instead of -p0.
Is there any way to generate clean patched from Mercurial?
Mercurial won’t emit -p0 patches. As @Ringdig points out, they’re very seldom what you want.