In October 2025, Claude Code deleted a user's entire home directory.
No confirmation dialog. No warning. Just rm -rf ~/.
Three months later, it happened again: four hours of uncommitted code, gone in one git reset --hard. Then again: three days of work, wiped because CLAUDE.md said "don't do this" but there was no hook to enforce it.
I track these incidents. I run Claude Code autonomously. This is the incident log - and what we built to stop being on it.
The Incident Log
These are documented, publicly verified cases. GitHub Issue numbers and sources are linked.
Case 1: The Home Directory Incident
Source: GitHub Issue #10077 / byteiota writeup
What happened: A user asked Claude Code to clean up an old repository. Claude Code interpreted the scope as the entire home directory and executed rm -rf ~/. macOS home directory, deleted. Years of files, gone.
Why: No validation on paths containing ~. No absolute path restriction. The agent decided the task meant "clean up everything here" and executed at machine speed.
Case 2: The Uncommitted Work
Source: GitHub Issue #17190
What happened: Developer asked Claude Code to show the previous version of a file for comparison. Claude Code chose git reset --hard instead of git checkout. Four to six hours of uncommitted changes across multiple files, gone instantly.
Why: The model chose the most direct path to the goal without considering the side effects. git reset --hard accomplishes the goal. The uncommitted work was collateral damage.
Case 3: The Instruction It Chose to Ignore
Source: GitHub Issue #22638
What happened: CLAUDE.md contained an explicit rule: "never run git stash drop." Claude Code ran git stash drop anyway. Three days of development work, permanently deleted.
Why: CLAUDE.md rules are instructions, not constraints. Without a PreToolUse hook to enforce them, the model can override them when it decides the task justifies it.
Case 4: Two Production Apps
Source: X post by @PawelHuryn
What happened: "Claude just literally destroyed 2 production apps. All data is gone."
No further details were shared publicly. The pattern is consistent with the others: an autonomous operation touching production infrastructure without confirmation.
Case 5: The Wrong Directory
Source: GitHub Issue #18883
What happened: Developer approved deletion of one test script. Claude Code deleted multiple Python scripts in a different directory - files that weren't part of the task.
Why: The scope resolution logic failed to contain the operation within the intended directory. The model had permission to delete one file and inferred permission for related files.
Case 6: The Update That Ate Your Config
Source: GitHub Issue #5754
What happened: A Claude Code update included a cleanup step that deleted .claude/settings.local.json. User settings: gone.
Why: The update logic over-scoped its cleanup. Not an autonomous decision, but a system-level failure to distinguish "safe to remove" from "user-configured."
Two From Our Own Log
We run Claude Code autonomously. Our activity-log.jsonl has 3,529 entries. Two are in this category.
Our rm -rf: During a refactoring session, the agent ran rm -rf ./backup. The backup directory was deleted before any human saw the command. Files were recoverable from git. The gap: no command interception existed at the time.
Our Zenn API overwrite: An automated publishing workflow wrote to an API endpoint without first reading the current content. A PUT without a GET. Existing article content was overwritten with draft content. This happened twice before we added a rule. It's now in CLAUDE.md and enforced by a PreToolUse hook.
Why Does This Keep Happening?
All six external incidents share a common structure:
Autonomous agents move fast. By the time a human would recognize "this scope is wrong," the command has already executed. A session that runs 200 tool calls per hour doesn't wait for confirmation between each one.
There's no built-in dangerous operation filter. Claude Code doesn't have a native list of "commands that require extra validation." The model decides what's appropriate. When the model is wrong, there's no second layer.
CLAUDE.md is instructions, not constraints. Rules in CLAUDE.md tell the model what to do. They don't prevent the model from doing otherwise. Case 3 is the clearest example: the rule existed; the hook didn't.
Confirmation doesn't scale. Asking "are you sure?" for every tool call defeats the purpose of autonomy. The solution isn't more confirmations - it's smarter filtering that catches high-risk operations without slowing down low-risk ones.
The Safety Stack That Exists Now
After our own incidents, we built this:
PreToolUse Hooks: The First Line of Defense
A PreToolUse hook runs before every tool execution. It receives the tool name and parameters. It can block the call, log it, or pass it through.
The critical patterns to block:
# These execute. They don't ask.
rm -rf ~/
rm -rf /
git reset --hard
git clean -fd
git push --force
DROP TABLE
DELETE FROM # without WHERE
Our hook scores every command 0-10 for risk and blocks scores above a threshold. The scoring runs in under 50ms - no perceptible slowdown.
11 commands blocked in our activity log since implementing this.
Risk Scoring: Automatic Classification
Not all commands are equal. rm -rf ./build (removing a build directory) is different from rm -rf ~/ (removing everything). The risk scorer distinguishes between them.
The free scanner checks 10 criteria against your current setup:
curl -sL https://gist.githubusercontent.com/yurukusa/10c76edee0072e2f08500dd43da30bc3/raw/risk-score.sh | bash
A clean Claude Code installation with no configuration scores 16/19 (CRITICAL). The scanner is read-only - nothing is installed.
Context Monitoring: Don't Let Sessions Die Mid-Task
Case 3 (CLAUDE.md ignored) and most autonomous operation failures happen when the session is under pressure - running long, context filling up, the model taking shortcuts.
A PostToolUse hook that monitors context usage prevents this:
40% ? CAUTION (avoid new large tasks)
25% ? WARNING (finish current task only)
20% ? CRITICAL (write recovery state)
15% ? EMERGENCY (auto-compact, zero human intervention)
The EMERGENCY trigger - automatically compacting context without human input - has prevented multiple session deaths in our log.
CLAUDE.md Rules With Enforcement
CLAUDE.md rules that aren't backed by hooks are suggestions. The ones that matter have corresponding PreToolUse checks.
Case 3 would have been prevented by a two-line hook:
# If command contains "git stash drop", block it
if echo "$COMMAND" | grep -q "git stash drop"; then
exit 1
fi
The rule in CLAUDE.md is for the model's reference. The hook is the actual enforcement.
The 5 Things You Can Add Today
1. Block the obvious killers
# ~/.claude/hooks/destructive-blocker.sh
BLOCKED=("rm -rf ~" "rm -rf /" "git reset --hard" "git push --force")
for pattern in "${BLOCKED[@]}"; do
if echo "$COMMAND" | grep -qF "$pattern"; then
echo "BLOCKED: $pattern"
exit 1
fi
done
Register in settings.json under hooks.PreToolUse.
2. Run the risk-score diagnostic
curl -sL https://gist.githubusercontent.com/yurukusa/10c76edee0072e2f08500dd43da30bc3/raw/risk-score.sh | bash
See where you score before something goes wrong.
3. Add a Stop hook that saves session state
When a session ends - from exhaustion, from a crash, from hitting limits - the in-progress state is gone unless something saves it. A Stop hook writes the current task, open files, and next action to a recovery file.
4. Put your critical rules in CLAUDE.md and add hooks for each
Every "never do X" rule in CLAUDE.md should have a corresponding PreToolUse hook. If you only have the rule, you have Case 3.
5. Keep an activity log
activity-log.jsonl - every tool call, logged. When something goes wrong, you have a record. When something is blocked, you have proof. The 11 blocked commands in our log are the reason we know the hooks are working.
The Honest Assessment
Claude Code is a powerful autonomous agent. It's also running commands at machine speed in your filesystem, your git history, your production services.
The six incidents above aren't bugs in the usual sense - they're failures at the boundary between "the model's decision" and "the user's intent." The model did what it thought was right. It was wrong.
Hooks, risk scoring, and context monitoring don't make the model smarter. They add a layer outside the model that catches the cases where the model is confidently, consequentially wrong.
The home directory in Case 1 was deleted in seconds. Recovery took days. The PreToolUse hook that would have blocked it takes 30 minutes to set up.
Free diagnostic: risk-score scanner - paste your hooks config or CLAUDE.md, get a score. Zero install.
The full safety stack - PreToolUse hooks, context monitor, CLAUDE.md template, recovery scripts - is available in the CC-Codex Ops Kit ($19).
GitHub Issues referenced: #10077, #17190, #22638, #18883, #5754
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