Missing User Warnings
Medium
- Confidence
- 95% confidence
- Finding
- The workflow explicitly instructs the agent to copy `scripts/md-sections.sh` into the user's project during Phase 0, which is a file-system modification before any explicit confirmation step. Silent project modification is dangerous because it can alter repositories, introduce unreviewed executable content, and create supply-chain or trust-boundary issues if the script content is unexpected or later executed.
