[MODEL] git stash/pop run for an unrelated build check silently destroyed the user's staged index

Preflight Checklist

• [x] I have searched existing issues for similar behavior reports
• [x] This report does NOT contain sensitive information (API keys, passwords, etc.)

Type of Behavior Issue

Claude reverted/undid previous changes without asking

What You Asked Claude to Do

I asked Claude to refactor a piece of code that was working around case-sensitivity instead of simply using C#'s IgnoreCase comparisons.

What Claude Actually Did

1. Claude made requested changes
2. Claude noticed potentially pre-existing build analyzer warnings it wanted to validate were pre-existing
3. As usual, Claude loves to git stash to confirm this (git stash -q -> dotnet build -> git stash pop)
4. The git pop operation discarded the index, destroying the user's manual work staging certain changes separately from the unstaged changes

Expected Behavior

Auto mode SHOULD HAVE BLOCKED the git operation, because it was destructive

Files Affected

Modified:
- My entire git index

Permission Mode

Accept Edits was ON (auto-accepting changes)

Can You Reproduce This?

Yes, every time with the same prompt

Steps to Reproduce

Any code work where Claude notices something at the final build and wants to verify it's pre-existing

Claude Model

Opus

Relevant Conversation

Impact

Critical - Data loss or corrupted project

Claude Code Version

2.1.229 (Claude Code)

Platform

Anthropic API

Additional Context

_No response_