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:

• I've reviewed my own diff for quality, security, and reliability
• Unsafe blocks (if any) have justifying comments
• The content is consistent with the UI/UX checklist
• Tests cover the new/changed behavior
• Performance impact has been considered and is acceptable

Closes #56225

Release Notes:

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