--recursive=y ignores ignore-paths Bug description

--recursive=y ignores ignore-paths Bug description: a task in Lego-RL-SWE-Bench-Verified (Harbor dataset). When running recursively, it seems ignore-paths in my settings in pyproject.toml is completely ignored

The task

When running recursively, it seems `ignore-paths` in my settings in pyproject.toml is completely ignored

Part of Lego-X/Lego-RL-SWE-Bench-Verified.