Claude Permissions Optimizer

Claude Permissions Optimizer

Find safe Bash commands that are causing unnecessary permission prompts and auto-allow them in settings.json -- evidence-based, not prescriptive.

This skill identifies commands safe to auto-allow based on actual session history. It does not handle requests to allowlist specific dangerous commands. If the user asks to allow something destructive (e.g., rm -rf, git push --force), explain that this skill optimizes for safe commands only, and that manual allowlist changes can be made directly in settings.json.

Pre-check: Confirm environment

Determine whether you are currently running inside Claude Code or a different coding agent (Codex, Gemini CLI, Cursor, etc.).

If running inside Claude Code: Proceed directly to Step 1.

If running in a different agent: Inform the user before proceeding:

> "This skill analyzes Claude Code session history and writes to Claude Code's settings.json. You're currently in [agent name], but I can still optimize your Claude Code permissions from here -- the results will apply next time you use Claude Code."

Then proceed to Step 1 normally. The skill works from any environment as long as ~/.claude/ (or $CLAUDE_CONFIG_DIR) exists on the machine.

Step 1: Choose Analysis Scope

Ask the user how broadly to analyze using the platform's blocking question tool (AskUserQuestion in Claude Code, request_user_input in Codex, ask_user in Gemini). If no question tool is available, present the numbered options and wait for the user's reply.

1. All projects (Recommended) -- sessions across every project
2. This project only -- sessions for the current working directory
3. Custom -- user specifies constraints (time window, session count, etc.)

Default to All projects unless the user explicitly asks for a single project. More data produces better recommendations.

Step 2: Run Extraction Script

Run the bundled script. It handles everything: loads the current allowlist, scans recent session transcripts (most recent 500 sessions or last 30 days, whichever is more restrictive), filters already-covered commands, applies a min-count threshold (5+), normalizes into Bash(pattern) rules, and pre-classifies each as safe/review/dangerous.

All projects:

node /scripts/extract-commands.mjs

This project only -- pass the project slug (absolute path with every non-alphanumeric char replaced by -, e.g., /Users/tmchow/Code/my-project becomes -Users-tmchow-Code-my-project):

node /scripts/extract-commands.mjs --project-slug 

Optional: --days to limit to the last N days. Omit to analyze all available sessions.

The output JSON has:

• green: safe patterns to recommend { pattern, count, sessions, examples }
• redExamples: top 5 blocked dangerous patterns { pattern, reason, count } (or empty)
• yellowFootnote: one-line summary of frequently-used commands that aren't safe to auto-allow (or null)
• stats: totalExtracted, alreadyCovered, belowThreshold, patternsReturned, greenRawCount, etc.

The model's job is to present the script's output, not re-classify.

If the script returns empty results, tell the user their allowlist is already well-optimized or they don't have enough session history yet -- suggest re-running after a few more working sessions.

Step 3: Present Results

Present in three parts. Keep the formatting clean and scannable.

Part 1: Analysis summary

Show the work done using the script's stats. Reaffirm the scope. Keep it to 4-5 lines.

Example:

## Analysis (compound-engineering-plugin)

Scanned **24 sessions** for this project.
Found **312 unique Bash commands** across those sessions.

- **245** already covered by your 43 existing allowlist rules (79%)
- **61** used fewer than 5 times (filtered as noise)
- **6 commands** remain that regularly trigger permission prompts

Part 2: Recommendations

Present green patterns as a numbered table. If yellowFootnote is not null, include it as a line after the table.

### Safe to auto-allow
| # | Pattern | Evidence |
|---|---------|----------|
| 1 | `Bash(bun test *)` | 23 uses across 8 sessions |
| 2 | `Bash(bun run *)` | 18 uses, covers dev/build/lint scripts |
| 3 | `Bash(node *)` | 12 uses across 5 sessions |

Also frequently used: bun install, mkdir (not classified as safe to auto-allow but may be worth reviewing)

If redExamples is non-empty, show a compact "Blocked" table after the recommendations. This builds confidence that the classifier is doing its job. Show up to 3 examples.

### Blocked from recommendations
| Pattern | Reason | Uses |
|---------|--------|------|
| `rm *` | Irreversible file deletion | 21 |
| `eval *` | Arbitrary code execution | 14 |
| `git reset --hard *` | Destroys uncommitted work | 5 |

Part 3: Bottom line

One sentence only. Frame the impact relative to current coverage using the script's stats. Nothing else -- no pattern names, no usage counts, no elaboration. The question tool UI that immediately follows will visually clip any trailing text, so this must fit on a single short line.

Adding 22 rules would bring your allowlist coverage from 65% to 93%.

Compute the percentages from stats:

• Before: alreadyCovered / totalExtracted * 100
• After: (alreadyCovered + greenRawCount) / totalExtracted * 100

Use greenRawCount (the number of unique raw commands the green patterns cover), not patternsReturned (which is just the number of normalized patterns).

Step 4: Get User Confirmation

The recommendations table is already displayed. Use the platform's blocking question tool to ask for the decision:

1. Apply all to user settings (~/.claude/settings.json)
2. Apply all to project settings (.claude/settings.json)
3. Skip

If the user wants to exclude specific items, they can reply in free text (e.g., "all except 3 and 7 to user settings"). The numbered table is already visible for reference -- no need to re-list items in the question tool.

Step 5: Apply to Settings

For each target settings file:

1. Read the current file (create { "permissions": { "allow": [] } } if it doesn't exist)
2. Append new patterns to permissions.allow, avoiding duplicates
3. Sort the allow array alphabetically
4. Write back with 2-space indentation
5. Verify the write -- tell the user you're validating the JSON before running this command, e.g., "Verifying settings.json is valid JSON..." The command looks alarming without context:

``bash node -e "JSON.parse(require('fs').readFileSync('','utf8'))" `` If this fails, the file is invalid JSON. Immediately restore from the content read in step 1 and report the error. Do not continue to other files.

After successful verification:

Applied N rules to ~/.claude/settings.json
Applied M rules to .claude/settings.json

These commands will no longer trigger permission prompts.

If .claude/settings.json was modified and is tracked by git, mention that committing it would benefit teammates.

Edge Cases

• No project context (running outside a project): Only offer user-level settings as write target.
• Settings file doesn't exist: Create it with { "permissions": { "allow": [] } }. For .claude/settings.json, also create the .claude/ directory if needed.
• Deny rules: If a deny rule already blocks a command, warn rather than adding an allow rule (deny takes precedence in Claude Code).

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: Jerrylalala
• Source: Jerrylalala/compound-engineering
• License: MIT

Install and usage instructions live in the source repository linked above.