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I let Claude Code audit its own setup.
It came back with 104 findings.

Find the context tax, dead permissions, MCP bloat, and zombie automations hiding in your Claude Code setup.

Current release: v0.13.0 — Example Manifest validation, Renderer Bug validation, Contributed Report validation, Linux beta probe plan, 60-second walkthrough generator, Windows beta probe plan, Cross-Harness Checkups, Community Domain Packs, CI Budget Gate, and Diff Mode. See CHANGELOG.md.

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The 104-Finding Checkup

Claude Code Doctor is a read-only checkup for the AI-workspace layer: the context, permissions, tools, skills, automations, and evidence trails that shape what your coding agent sees before it writes a single line. Patient zero was my own two-year Claude Code setup:

What	Found
Always-on context loaded every session	45,000 tokens (22.5% of the window, gone before work starts)
Permission allow-list entries	804, of which 77 pointed at paths that no longer exist
MCP tools injected every session	63, including two servers that fully overlap
Zombie automations failing silently every morning	12
Skills with colliding trigger words	several clusters across 70 skills
Reclaimable disk found along the way	~200 GB

Your setup is different. That's the point. Linters audit your code; this audits the environment that tells your AI what "normal" is.

Paste This Into Claude Code

Use this if you want the safest first run:

I want to run Claude Code Doctor as a read-only setup audit.
First confirm the scan scope, no-go paths, and exactly one report destination.
Do not change files, settings, git state, automations, permissions, or secrets before I approve.
Then run the 10-domain audit, produce the Markdown report, render the HTML dashboard, and give me matrix-A/B prescriptions.

Short form:

audit my claude code setup, read-only. no changes before I approve.

or simply /doctor.

Demo In 10 Seconds

Preview the renderer without scanning your machine:

python3 scripts/build_dashboard.py samples/dashboard.json /tmp/claude-code-doctor-dashboard.html
open /tmp/claude-code-doctor-dashboard.html

Generate sanitized share-card PNGs from fictional fixture data:

python3 scripts/build_share_cards.py samples/share-cards.json /tmp/claude-code-doctor-cards/
open /tmp/claude-code-doctor-cards/

All sample data is fictional. Your real report is generated locally and never leaves your machine.

60-Second Walkthrough

Generate a short narration script and HTML capture surface:

python3 scripts/build_walkthrough.py docs/generated-demo
open docs/generated-demo/demo-walkthrough.html

The script is also available as docs/walkthrough.md.

Diff Mode

The real point of a checkup is the next checkup. Compare two exported reports:

python3 scripts/compare_reports.py samples/diff-before.json samples/diff-after.json /tmp/claude-code-doctor-diff.md
open /tmp/claude-code-doctor-diff.md

The diff report shows score deltas, always-on token drift, permission drift, MCP tool drift, resolved/new red flags, finding movement, and prescription progress.

CI Budget Gate

Fail CI when a sanitized report exceeds your team budget:

python3 scripts/check_budgets.py samples/diff-before.json samples/budgets.json /tmp/claude-code-doctor-budget.md
open /tmp/claude-code-doctor-budget.md

Budgets can cap always-on tokens, permission entries, MCP tools, and critical findings. See docs/ci-budget-gate.md.

Contributed Reports

Validate sanitized real-world grade reports before posting them publicly:

python3 scripts/validate_contributed_report.py samples/contributed-report.json

The validator accepts aggregate metrics only and rejects raw paths, emails, and secret-shaped strings. See docs/contributed-reports.md.

Renderer Bug Reports

Validate minimal fictional renderer repros before opening a public bug report:

python3 scripts/validate_renderer_bug.py samples/renderer-bug-dashboard.json

The validator keeps dashboard/share-card bugs reproducible without raw local reports, private paths, or secrets. See docs/renderer-bug-reports.md.

Example Manifest

Validate that public examples exist, stay fictional, and have proof commands:

python3 scripts/validate_examples_manifest.py docs/examples-manifest.json

The manifest keeps samples and generated demos useful without teaching people to publish raw local reports. See docs/examples.md.

Community Domain Packs

Validate optional read-only check packs before using or contributing them:

python3 scripts/validate_domain_pack.py domain-packs/security-team.md
python3 scripts/validate_domain_pack.py domain-packs/*.md

Included packs cover security teams, solo founders, teaching workshops, and locked-down enterprise environments. See docs/domain-packs.md.

Cross-Harness Checkups

Validate adapter notes for Claude Code, Codex, Cursor, and OpenCode-style workbenches:

python3 scripts/validate_adapter_notes.py docs/adapters/*.md

Adapters keep the same vocabulary for context tax, permission drift, tool tax, automation drift, red flags, and prescriptions. See docs/cross-harness.md.

Linux Beta

Generate a reviewable read-only shell plan before scanning Linux or WSL:

python3 scripts/build_linux_probe_plan.py /tmp/claude-code-doctor-linux.md
open /tmp/claude-code-doctor-linux.md

The plan maps all 10 domains to Linux-safe probes such as find, du, crontab -l, systemctl --user list-timers, and ss -ltnp. See docs/linux.md.

Windows Beta

Generate a reviewable read-only PowerShell plan before scanning Windows:

python3 scripts/build_windows_probe_plan.py /tmp/claude-code-doctor-windows.md
open /tmp/claude-code-doctor-windows.md

The plan maps all 10 domains to Windows-safe probes such as Get-ChildItem, Get-ScheduledTask, and schtasks /Query. See docs/windows.md.

Quick Start

git clone https://github.com/kgraph57/claude-code-doctor.git ~/.claude/skills/claude-code-doctor

One command: cloning straight into your skills directory is the whole install (~/.claude/skills/ exists on any machine where Claude Code has run; prefer keeping repos elsewhere? clone anywhere and symlink instead).

Requirements: none for the audit and Markdown report. The HTML dashboard uses only the Python standard library. Share-card PNGs (optional) need headless Chrome/Chromium + Pillow.

Linux: beta coverage is available as a read-only shell probe plan — see docs/linux.md. Domain 9 swaps launchd for cron/systemd timers, and plutil checks are macOS-only. Share cards work with Chromium. Windows: beta coverage is available as a read-only PowerShell probe plan — see docs/windows.md.

Why Star This Repo?

Star it if you want this to become the standard safety layer for agentic coding setups:

• Monthly checkups: run the same audit repeatedly, like an annual physical for your AI workspace
• Diff mode: compare your current setup against the last checkup and prove the cleanup worked — shipped in v0.4.0
• CI budget gates: fail a PR when always-on context, permissions, or tool tax drifts past a budget — shipped in v0.5.0
• Community domain packs: add checks for teams, frameworks, OSes, and security policies without forking the core skill — shipped in v0.6.0
• Cross-harness checkups: adapt the same protocol to Claude Code, Codex, Cursor, and other agent workbenches — shipped in v0.7.0

See the full build path in docs/roadmap.md.

Why this exists

Claude Code setups grow like gardens. Every skill you add, every permission you approve, every MCP server you try stays behind — and nobody ever looks back. An unhealthy setup means an unhealthy AI: bloated with config it drags into every session, slow to start, prone to weird moves. You are raising this thing — keep it fit.

How it works

The whole trick is one separation: diagnosis is strictly read-only, treatment happens only after you approve each fix. Coverage comes from cheap models fanned out in parallel; judgment stays on the strong model; decisions stay with you.

What you get

All report screenshots below show fictional sample data — your report is generated locally from your own machine and never leaves it.

A checkup report, like the one from your annual physical. Each of the ten domains gets a 0-100 score and an A-E grade (A "healthy" through E "treat now"), plotted on a 10-axis radar chart. An optional body-map mode adds the organ metaphor (CLAUDE.md as the brain, settings as the heart) for shareable reports — plain domain names by default. Critical dangers — plaintext credentials, private files tracked by git — are red flags that force a failing grade no matter the arithmetic. The scoring model is fully documented in references/scoring.md:

A prescription, not just a diagnosis. Every fix ships as an action card: risk level (safe / careful / surgery), time estimate, expected effect, and a ready-to-paste prompt — copy it into Claude Code and exactly that one fix runs, with backup and quarantine baked in. Checkboxes persist in your browser, so the report doubles as your progress tracker:

A one-page HTML dashboard — stat band, the decisions only you can make (as OPTION A/B), an impact-x-effort matrix, a phased fix plan, and every finding as collapsible evidence + proposal:

Sanitized share cards (optional) — brag about your findings without leaking your paths. Generated by the same scripts, with automatic path masking:

What gets checked

Ten domains, each with an explicit checklist you can review (and veto) before the scan — full definitions in references/domains.md:

#	Domain	Examples of what it looks for
1	Directory structure	files parked in ~/ for years, dead dot-folders, Desktop/Downloads backlog
2	Dev repositories	stray repos, bloated .git packs, nested/circular clones, missing CI
3	CLAUDE.md hierarchy	the always-on token tax (as a number), duplication, stale dated notes
4	Settings & permissions	dead allow entries, plaintext credentials, guardrail gaps, unscoped rules
5	Skills	trigger-word collisions, misfire-prone descriptions, oversized single files
6	Commands	command/skill duplicates that diverged, same name with different behavior
7	Subagents	unpinned models (silent cost leak), reviewers holding Write access, dormant teams
8	MCP & plugins	per-session tool tax, overlapping servers, ghost configs, dead ports
9	Automations & git	cron/launchd zombies pointing at vanished paths, unrotated logs, stale branches
10	Usage & disk	transcript remains, node_modules inside skills, oversized sessions

Safety by design

• Read-only by prompt contract — the mutation ban is baked into every subagent prompt. Be clear about what that means: it is an instruction-level contract, not an OS sandbox. For hard guarantees, pair it with Claude Code permission deny rules; the skill treats a firing guard as a stop signal, never something to route around
• No-go paths — folders you designate are never read, not even traversed
• Secrets are never quoted — path and existence only
• Nothing is deleted — fixes quarantine files with a manifest; deletion comes weeks later
• Nothing leaves your machine — no telemetry, no uploads; share cards are opt-in and sanitized (emails, API-key shapes, tokens, UUIDs and user paths auto-masked, and rendering fails closed if anything secret-shaped survives). The masking is a seatbelt, not a guarantee — glance at a card before you post it
• If a permission guard blocks a fix, the skill stops and reports instead of routing around it

The philosophy

An AI workspace checkup is not a cleanup script. It is a clinical protocol for trustworthy delegation: measure the hidden context, permissions, tools, automations and evidence trails that shape what your AI does before you let it act. The short version is: diagnose first, treat only after consent, and make every finding inspectable. See docs/ai-checkup-philosophy.md.

The principles baked in

This repo doubles as a working example of frontier-model best practices in Claude Code — built with and battle-tested on Claude Fable 5 and Opus 4.8, and a good first thing to run if you just got Fable 5 access and wonder where your context budget goes. See docs/best-practices.md:

1. Decide the shape of the work before you fire the model
2. Read-only parallel fan-out, top-tier synthesis
3. Force structured output
4. Separate diagnosis from treatment (user sovereignty)
5. Carry deliverables to "showable" — and verify rendering before calling it done
6. Always-on context is rent: measure it, then cut it

FAQ

Does it change anything on my machine?

Not during diagnosis. The audit writes exactly one report file, to a location you approve first. Fixes run only after you explicitly approve each one, with backups and quarantine instead of deletion.

Does my data go anywhere?

No. Everything runs locally through your own Claude Code session. The share cards are an opt-in feature, and they sanitize aggregates only.

How long does it take?

Patient zero (a two-year-old heavy setup) took about 12 minutes with 10 parallel subagents. Sequential fallback takes longer.

What does the audit itself cost?

Patient zero (a two-year heavy setup, 10 parallel subagents) consumed roughly one million tokens end to end — a few dollars at API prices, or a meaningful chunk of a subscription session. The sequential fallback spends less at once but takes longer. A tool that flags your cost leaks should disclose its own price tag.

Can I run it in a locked-down corporate environment?

Everything runs locally inside your own Claude Code session; the skill adds no network calls and no telemetry of its own. It respects your permission settings — if your deny rules block a probe, the auditor reports the gap instead of working around it.

Does it work in Japanese?

Yes — reports and the dashboard follow your language (meta.lang: "en" | "ja"). The skill itself is bilingual-triggered.

Roadmap

• Health score (0-100), A-E grades, radar chart, red flags — shipped
• 60-second walkthrough generator and capture page — shipped
• Diff mode: compare against your last checkup (the real point of a checkup) — shipped
• Contributed report validator: share real grades without leaking raw paths — shipped
• Renderer bug validator: submit minimal fictional repro fixtures — shipped
• Example manifest validator: keep public examples safe and reproducible — shipped
• Linux path coverage beta: read-only shell probe plan — shipped
• Windows path coverage beta: read-only PowerShell probe plan — shipped
• CI mode: fail a PR when the always-on token tax crosses a budget — shipped
• Community domain packs: add your own checks via validated Markdown packs — shipped

Contributions welcome — issues and PRs, in English or Japanese. See CONTRIBUTING.md.

If this helped

If it saved you tokens, money, or a weekend of cleanup, a ⭐ helps other people find it — and an issue with your overall grade helps calibrate the scoring model.

License

MIT — © 2026 Ken Okamoto, pediatrician & AI builder, Tokyo.