Add case study for issue #1161: Auto-restart uncommitted changes handling

[konard]

Summary

This PR adds a comprehensive case study analyzing issue #1161, where the auto-restart mechanism with a tool agent led to committing files that were not explicitly requested by the user.

📋 Issue Reference

Fixes #1161

🔍 Problem Analyzed

When the AI tool agent completed its work session with uncommitted files (temporary research data files), the auto-restart mechanism triggered a new session that committed and pushed these files to the pull request. These files were:

• Not part of the original requirements
• Not explicitly requested by the user
• Temporary research artifacts that should have been discarded

📝 Case Study Contents

The case study includes:

1. Timeline of Events - Detailed reconstruction of what happened
2. Root Cause Analysis - Why the auto-restart mechanism lacks discrimination between legitimate code and research artifacts
3. 5 Proposed Solutions:
   • File classification logic
   • Auto-discard research artifacts
   • Enhanced agent prompt guidance
   • .gitignore patterns for research files
   • Discard-by-default (conservative approach)
4. Industry Best Practices - Research from Anthropic, Block/Goose, and others on AI agent code change management
5. Full Logs - Execution logs and PR comments for reference

📁 Files Added

docs/case-studies/issue-1161/
├── README.md                              # Main case study analysis
├── pr-9-all-comments.txt                 # PR comments from the affected repository
└── solution-draft-log-pr-9-gristwidgets.txt  # Full execution log (1.3MB)

🔗 References

• Original Issue: Auto-restart with tool agent led to upload to files, that was not explicitly asked by user or requirements #1161
• Affected External PR: Создай новый виджет в папке edittable veb86/GristWidgets#9
• Full Log Gist: https://gist.github.com/konard/98f44cb214fbd473a9a58013de86a526

✅ What's Next

This case study documents the problem and proposes solutions. Implementation of the fixes would be handled in a separate PR.

[konard]

🤖 Solution Draft Log

This log file contains the complete execution trace of the AI solution draft process.

💰 Cost estimation:

• Public pricing estimate: $4.814794 USD
• Calculated by Anthropic: $2.914895 USD
• Difference: $-1.899899 (-39.46%)
  📎 Log file uploaded as Gist (710KB)
  🔗 View complete solution draft log

---

Now working session is ended, feel free to review and add any feedback on the solution draft.