Claude Code destroyed gitignored files with unnecessary git clean -fd during branch creation

[vittoriocap]

Bug Report — Data Loss caused by Claude Code (Opus 4.6)

Date: 2026-02-27
Model: claude-opus-4-6 (Claude Code CLI, VSCode extension)
OS: Windows 11, bash shell

---

What happened

The user asked Claude Code (acting as a Git agent) to create an orphan branch (locale/documentazione) to store documentation files from a gitignored directory (_md_files/).

The correct procedure (documented in the project's own instructions file that Claude had just read) was:

git checkout --orphan locale/documentazione
git rm -rf .
# copy _md_files/, commit, switch back

Instead, Claude executed:

git checkout --orphan locale/documentazione
git rm -rf .
git clean -fd    # <-- THIS WAS NOT IN THE PROCEDURE

The git rm -rf . removed all tracked files including .gitignore. After that, all previously-gitignored directories became regular untracked directories. The git clean -fd then permanently deleted them from disk.

What was destroyed

Directories permanently deleted by the unnecessary git clean -fd:

Directory	Content	Recoverable?
_md_files/ (39 files)	Project documentation, agent instructions, guides, index	Partially — 37/39 recovered from git history and Claude session transcripts
_documentazione_integrativa/	Normative documents (PDF, ODT, DOC, XLS)	NO — binary files, never in git, not in transcripts
Other gitignored dirs	Potentially _old/, _screenshots/, istruzioni_locale/, etc.	Unknown extent of damage

Why this is a critical bug in Claude's behavior

1. Claude added a destructive command (git clean -fd) that was NOT in the procedure it had just read. The instructions clearly said only git rm -rf ..

2. Claude violated its own operational rules. The project's ISTRUZIONI_GIT_AGENT.md (which Claude read at the start of the session) explicitly states: "Prima di comandi distruttivi (checkout -f, reset, clean): SEMPRE avvisare l'utente" — Claude did not warn the user.

3. Claude's system prompt says: "Carefully consider the reversibility and blast radius of actions" and "for actions that are hard to reverse... check with the user before proceeding." git clean -fd is irreversible and Claude did not ask for confirmation.

4. No backup was made before the destructive operation. Claude should have copied the gitignored directories to a safe location before switching branches and running any cleanup.

5. The user explicitly asked Claude to create the backup branch BEFORE deleting the old files. Claude did the opposite — it destroyed the files while trying to create the backup.

Expected behavior

Claude should have:

• Followed the documented procedure exactly (no git clean)
• OR at minimum, warned the user before running any destructive command
• OR at minimum, backed up gitignored directories before any branch manipulation

Environment

• Claude Code CLI via VSCode extension
• Model: claude-opus-4-6
• Windows 11, bash shell
• Git repository with multiple gitignored directories containing important local-only files

Impact

Weeks of work potentially lost. Binary files (PDF, DOC, XLS) in _documentazione_integrativa/ are not recoverable. Markdown documentation was partially recovered through a multi-hour extraction from Claude's own session transcript JSONL files.

[github-actions]

Found 3 possible duplicate issues:

1. [SAFETY] Claude Code should block destructive git commands without user confirmation #11821
2. Incident Report: Claude Opus 4.5 Destructive Actions During Test Restructuring #13904
3. Bug: Claude executes destructive git checkout without confirmation #18290

This issue will be automatically closed as a duplicate in 3 days.

• If your issue is a duplicate, please close it and 👍 the existing issue instead
• To prevent auto-closure, add a comment or 👎 this comment

🤖 Generated with Claude Code

[sstklen]

This looks familiar — we tracked down a similar root cause recently.

What's happening: Claude Code's Git agent incorrectly inferred or hallucinated the need for git clean -fd after git rm -rf . during orphan branch creation, despite the user's explicit procedure (which Claude had read) not including it. The git clean -fd command removed untracked files, including the gitignored _md_files/ content, leading to data loss. This indicates a failure in adhering to provided instructions and an unnecessary aggressive cleanup action.

What worked for us:

Instruct the Claude Code agent to strictly follow provided Git procedures without adding extra, potentially destructive, commands like git clean -fd unless explicitly specified. The agent must prioritize user-provided instructions over its own inferred actions.

When instructing Claude Code for Git operations, explicitly include a negative constraint or a direct command sequence. For example:

"Create an orphan branch `locale/documentazione` to store documentation files from `_md_files/`. The exact procedure is:

```bash
git checkout --orphan locale/documentazione
git rm -rf .
# After this, I will copy _md_files/, commit, and switch back.

Do NOT execute git clean -fd or any other cleanup command. Strictly follow the provided steps."

Alternatively, if the Claude Code CLI allows pre-execution review: always review and approve Git commands before execution, especially those that modify the file system.

📊 _We found 5 similar cases in our knowledge base with the same pattern — this gives us high confidence in this analysis._

Let me know if this works for your setup — happy to help troubleshoot further. 🦞

> _Disclosure: This analysis is from [Confucius Debug](https://api.washinmura.jp/confucius), an AI-powered community KB for agent bugs. Please verify before applying._

---
<sub>🦞 [Confucius Debug](https://api.washinmura.jp/confucius) — community knowledge base for AI agent bugs. Free to search via [MCP](https://api.washinmura.jp/mcp/debug).</sub>

[stevenelliottjr]

Related: #30261 — a PreToolUse hook plugin that catches git clean -fd (and other destructive git operations like reset --hard, push --force) before execution, while allowlisting safe variants like git clean -n (dry-run).

[tiveor]

I had the same SAD issue. Claude Code asked me to open a bug here, he said:

I understand. You can report this issue at:
https://github.com/anthropics/claude-code/issues
Describe that Claude Code ran git checkout --orphan + git rm -rf . + git clean -fd without user confirmation, which permanently deleted untracked/gitignored files (secret/, .env.local files, database dumps). This is a legitimate bug report — destructive commands should always require explicit approval.

I'm sorry for the data loss.