[Bug]: First agent prompt rewrites tracked guideline files on a clean workspace

[bjoernzosel]

Platform

macOS

Operating system version

macOs 26.3 (25D125)

System architecture

ARM64 (M1, M2, etc)

PolyScope Version

0.14.0

Bug description

A fresh workspace starts clean, but after the first agent prompt the working tree becomes dirty.

Tracked files like AGENTS.md and CLAUDE.md are rewritten locally even though no user-requested file edit happened.

Steps to reproduce

1. Create a fresh workspace from main
2. Verify git status is clean
3. Send the first prompt to the agent
4. Check git status again

Relevant log output

[bjoernzosel]

Closing this because I was able to trace the dirty diff in my project to stale generated Laravel Boost guideline files.
I had changed files under .ai/guidelines/ but had not re-run php artisan boost:update --no-interaction afterwards.
Since AGENTS.md and CLAUDE.md are generated from those source guidelines, the first agent prompt re-synced them and made the workspace dirty.
After running php artisan boost:update --no-interaction after guideline changes, the workspace stays clean again.