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It fixes the issue #176 and the PR #177. PR #177 was almost fine. The idea of the PR was to force src and dst prefix. The problem was that, to generate patch for new files, we diff the new file against /dev/null. git does not like prefix for out of repository files. The simple fix is to always force --no-prefix. To make it work, git apply must use -p0 option: this option tells that there is no prefix in the src dst files paths.
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