Fix patches being reversed if repo state in container differs from base_commit

[ludwig-n]

This applies the fix from this upstream PR: SWE-bench#453. This fixes issue SWE-bench#228 which was causing Sphinx instances to fail with patches produced by OpenHands.

Score changes as a result of the fix:

• Qwen3-Coder-30B-A3B + OpenHands: 45.1 -> 48.3 (average of 3 runs).

Problem description:

• In some SWE-bench containers, in particular for some/all instances from the sphinx-doc/sphinx repo, the repository folder /testbed contains additional changes compared to the base_commit listed in the HuggingFace dataset.
• OpenHands creates patches by running git diff relative to the listed base_commit. Therefore, these patches already contain the additional changes mentioned above.
• When these patches are applied using the patch --batch command, it incorrectly assumes the patches are reversed and reverts the files back to the state they were in at base_commit, which is wrong and causes the tests to fail, but the patch is reported as "successfully applied".