fix: Remove nested git repositories before adding files in SWE-bench

[magic3007]

Problem
In SWE-Bench-like benchmark, the agent may create a .git repository in the local directory when reproducing the error (e.g., the case iterative__dvc-5336 in swe-gym-lite benchmark). As a result, an error would occur when I executed git add -A later.

[xingyaoww]

Thanks! I'll do some testing to see if it breaks normal eval, if not - I'll merge it!