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git apply does not work from within the local checkout of an unrelated git repository

As freshly documented at http://drupal.org/patch/apply

git apply will fail to do anything when used within a local checkout of a git repository (other than the one for the project the patch is made for), such as if you are patching a module that is within a site that is in Git version control. Use patch -p1 < path/file.patch instead.

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