The tool definition is very clearly contradicting the previous behavior.
Performance impact is unclear to me, we increase the work in a
potentially expensive loop, but it seems necessary to have both the
specified behavior from the tool definition, as well as the
heuristic/fallback for misbehaving models that seems to be intended.

Self-Review Checklist:

- [X] I've reviewed my own diff for quality, security, and reliability
- [X] Unsafe blocks (if any) have justifying comments
- [X] The content is consistent with the [UI/UX
checklist](https://github.com/zed-industries/zed/blob/main/CONTRIBUTING.md#uiux-checklist)
- [X] Tests cover the new/changed behavior
- [X] Performance impact has been considered and is acceptable

Closes #56225

Release Notes:

- Fixed tool paths preferring files in subdirectories named after the
project root