[Bug] Claude Code ignores user instruction to preserve local files during git-filter-repo operation

Bug Description

Claude Code deleted local files despite explicit instruction to preserve them.

User Request

Asked to remove large embedding files (~2.8GB) from Git tracking/history, explicitly stating:

"_remove from tracking/Git, but I don't want the local files deleted in the process_."

What Claude Did Wrong

Claude ran git-filter-repo --path scriptures/embeddings/ --invert-paths --force without first backing up the local files to a safe location. This command rewrites Git history AND removes the files from the working directory.

Correct Approach

Claude should have:

1. Copied the embeddings folder to a temporary location (e.g., cp -r scriptures/embeddings/ /tmp/embeddings_backup/)
2. Run git-filter-repo
3. Restored the files from the backup

Consequence

We lost ~2.8GB of OpenAI-generated embeddings that cost real money to produce. No local backup existed, and Time Machine was not available.

Root Cause

Claude proceeded with a destructive operation without implementing the safeguard explicitly requested. Claude acknowledged the requirement in the response ("I'll remove them from Git history while preserving your local files") but failed to execute a backup step before running the destructive command.

Environment Info

| Field | Value |
| ----------- | -------------------------------------- |
| Platform | darwin |
| Terminal | Apple_Terminal |
| Version | 2.1.4 |
| Feedback ID | 8f735022-38dc-421c-a543-beb1026c85a0 |