project-health

Project Health

One skill for everything about your project's Claude Code configuration. Run it at the start, middle, or end of a project — it figures out what's needed.

Goal: Zero permission prompts, well-organised context files, no cruft.

When to Use

| You say... | What happens | |-----------|-------------| | "project health" / "check project" | Full audit: permissions + context + docs | | "setup project" / "kickoff" / "bootstrap" | New project setup from scratch | | "tidy permissions" / "clean settings" | Fix permissions file only | | "capture learnings" / "update CLAUDE.md" | Save session discoveries | | "add python" / "add docker permissions" | Add a preset to existing settings | | "audit context" / "audit memory" | Context-focused audit only |

Architecture: Sub-Agents

Heavy analysis runs in sub-agents to keep the main conversation clean. The main agent orchestrates; sub-agents do the scanning and return summaries.

Agent 1: Permission Auditor

Launched with Task(subagent_type: "general-purpose"). Prompt:

Read .claude/settings.local.json.

**Discover connected MCP servers**: Use ToolSearch (search "mcp") and extract unique
server prefixes from tool names (e.g. mcp__vault__secret_list → vault).

**Discover installed skills**: Use the Skill tool or ToolSearch to list available skills.
For each skill that has scripts/ in its directory, note what Bash patterns it needs
(python3, env var prefixes like GEMINI_API_KEY=*, etc.). Check the SKILL.md for any
MCP tools the skill references (e.g. mcp__vault__secret_get).

Report:
1. MCP servers connected but NOT in settings (missing)
2. MCP servers in settings but NOT connected (stale)
3. Skill permissions: Bash patterns and MCP tools that installed skills need but aren't approved
4. File access: check for Read/Edit/Write patterns for .claude/** and //tmp/**
   in project settings, and ~/Documents/**/~/.claude/** in global settings
5. Leaked secrets: entries containing API keys, tokens, bearer strings, hex >20 chars, base64 >20 chars
6. Legacy colon syntax: entries like Bash(git:*) instead of Bash(git *)
7. Junk entries: shell fragments (Bash(do), Bash(fi), Bash(then), Bash(else), Bash(done)),
   __NEW_LINE_* artefacts, loop body fragments (Bash(break), Bash(continue), Bash(echo *))
8. Duplicates: entries covered by a broader pattern (e.g. Bash(git add *) redundant if Bash(git *) exists)
9. Missing presets: based on files present, suggest presets from [permission-presets.md]

Prefer Read/Glob/Grep tools over Bash. If you need to scan multiple files or
run 3+ commands for one analysis, write a Python script to .jez/scripts/
and run it once (mkdir -p .jez/scripts first).

Return a structured summary, not raw data.

Agent 2: Context Auditor

Launched with Task(subagent_type: "general-purpose"). Prompt:

Audit the project context landscape at [repo-path]:

1. Find all CLAUDE.md files. For each:
   - Count lines (target: root 50-150, subdirs 15-50)
   - Score quality on 6 criteria (see quality-criteria.md)
   - Check for stale file/path references
   - Flag oversized files

2. Find .claude/rules/ topic files. Check sizes (target: 20-80 lines).

3. Detect project type from files present (see project-types.md).
   Check expected docs exist (ARCHITECTURE.md, DATABASE_SCHEMA.md, etc.)

4. Find public markdown (README.md, LICENSE, CONTRIBUTING.md).
   Check for overlap with CLAUDE.md content.

5. Check auto-memory at ~/.claude/projects/*/memory/MEMORY.md

6. If Cloudflare project: find all wrangler.jsonc/wrangler.toml files.
   Check each has "observability": { "enabled": true }. Flag any missing it.

Prefer Read/Glob/Grep tools over Bash. If you need to scan many files or
aggregate data across the repo, write a Python script to .jez/scripts/
and run it once rather than running many individual bash commands
(mkdir -p .jez/scripts first).

Return: project type, quality scores, missing docs, stale refs, overlaps,
size violations, observability gaps, and total markdown footprint.

Parallel Execution

For a full health check, launch both agents in parallel:

Task(subagent_type: "general-purpose", name: "permission-audit", prompt: "...")
Task(subagent_type: "general-purpose", name: "context-audit", prompt: "...")

Both return summaries. The main agent combines them into one report and proposes fixes.

Mode 1: Full Health Check

The default. Run this anytime.

Steps

1. Launch Permission Auditor and Context Auditor agents in parallel
2. Combine findings into a single report:

``` ## Project Health Report

Project type: [detected type] CLAUDE.md quality: [score]/100 ([grade])

### Permissions

• Missing MCP servers: [list]
• Leaked secrets: [count] found
• Legacy syntax: [count] entries
• Missing presets: [list]

### Context

• Oversized files: [list]
• Stale references: [list]
• Missing docs: [list]
• Overlaps: [list]

### Recommended Fixes

1. [fix 1]
2. [fix 2] ... ```

1. Apply fixes after single yes/no confirmation

Mode 2: New Project Setup

When: No .claude/settings.local.json exists, or user says "setup" / "kickoff".

Steps

1. Detect project type from files present:

| Indicator | Type | Preset | |-----------|------|--------| | wrangler.jsonc or wrangler.toml | cloudflare-worker | JS/TS + Cloudflare | | vercel.json or next.config.* | vercel-app | JS/TS + Vercel | | astro.config.* | astro | JS/TS + Static Sites | | package.json (no deploy target) | javascript-typescript | JS/TS | | pyproject.toml or setup.py or requirements.txt | python | Python | | Cargo.toml | rust | Rust | | go.mod | go | Go | | Gemfile or Rakefile | ruby | Ruby | | composer.json or wp-config.php | php | PHP | | pom.xml or build.gradle* | java | Java/JVM | | *.sln or *.csproj | dotnet | .NET | | mix.exs | elixir | Elixir | | Package.swift | swift | Swift + macOS | | pubspec.yaml | flutter | Mobile | | Dockerfile or docker-compose.yml | docker | Docker | | fly.toml or railway.json or netlify.toml | hosted-app | Hosting Platforms | | supabase/config.toml | supabase | Hosting + Database | | .claude/agents/ or operational scripts | ops-admin | — | | Empty directory | Ask the user | — |

Types stack (e.g. cloudflare-worker + javascript-typescript).

1. Generate .claude/settings.local.json:
2. Read [references/permission-presets.md](references/permission-presets.md)
3. Always include Universal Base (includes file access for .claude/**, //tmp/**)
4. Add detected language + deployment presets
5. Check if global ~/.claude/settings.local.json has home-relative file access patterns (~/Documents/**, ~/.claude/**). If not, suggest adding them there (NOT in the project file — home paths belong in global settings only)
6. Launch Permission Auditor agent to discover MCP servers and add per-server wildcards
7. Always include WebSearch, WebFetch
8. Always include explicit gh subcommands (workaround for Bash(gh *) bug)
9. Write with // comment groups

1. Generate CLAUDE.md:
2. Read [references/templates.md](references/templates.md)
3. Use project-type-appropriate template

1. Generate .gitignore:
2. Read [references/templates.md](references/templates.md)
3. Always include .claude/settings.local.json, .claude/plans/, .jez/screenshots/, .jez/artifacts/
4. Do NOT gitignore .jez/scripts/ — generated scripts are worth keeping

1. Optionally (ask first): git init + gh repo create

1. Warn: "Project settings.local.json SHADOWS global settings (does not merge). Session restart needed."

Mode 3: Tidy Permissions

When: User says "tidy permissions" or health check found permission issues.

Launch the Permission Auditor agent, then apply its recommended fixes.

Mode 4: Capture Learnings

When: End of session, "capture learnings", "save what we learned".

This runs in the main context (not a sub-agent) because it needs access to the conversation history.

1. Review conversation for discoveries worth preserving
2. Decide placement: ``` Applies to all projects? ├── YES → ~/.claude/rules/<topic>.md └── NO → Specific to a subdirectory? ├── YES → <dir>/CLAUDE.md └── NO → Reference or operational? ├── Reference → docs/ or ARCHITECTURE.md └── Operational → ./CLAUDE.md (root) ```
3. Draft all changes as diffs in a single batch
4. Apply after single yes/no confirmation

Keep it concise: one line per concept.

Mode 5: Add Preset

When: "add python permissions", "add docker", "add MCP servers".

1. Read the preset from [references/permission-presets.md](references/permission-presets.md)
2. Read existing .claude/settings.local.json
3. Merge without duplicating
4. Remind: session restart required

Mode 6: Restructure Context

When: Root CLAUDE.md over 200 lines, "restructure memory".

1. Launch Context Auditor agent first
2. Based on findings:
3. Split oversized CLAUDE.md into .claude/rules/<topic>.md
4. Extract directory-specific content to sub-directory CLAUDE.md
5. Move reference material to docs/
6. Resolve overlaps
7. Create missing docs for project type
8. Present plan, apply after approval

Size Targets

| File | Target | Maximum | |------|--------|---------| | Root CLAUDE.md | 50-150 lines | 200 | | Sub-directory CLAUDE.md | 15-50 lines | 80 | | Rules topic file | 20-80 lines | 120 |

Permission Syntax Quick Reference

| Pattern | Meaning | |---------|---------| | Bash(git *) | Preferred — space before * = word boundary | | Bash(nvidia-smi) | Exact match, no arguments | | WebFetch | Blanket web fetch | | WebSearch | Blanket web search | | mcp__servername__* | All tools on one MCP server |

What Does NOT Work

| Pattern | Why | |---------|-----| | mcp__* | Wildcard doesn't cross __ boundary | | mcp__*__* | Still doesn't work | | Bash(git:*) | Deprecated colon syntax (works but prefer space) |

Important Behaviours

• Not hot-reloaded: settings.local.json edits need session restart
• "Don't ask again" injects at runtime (no restart) using colon format — normal
• Shadows, not merges: Project settings completely replace global
• gh bug: Bash(gh *) sometimes misses subcommands — include explicit Bash(gh issue *) etc.

Autonomy

• Just do it: Detect project type, launch audit agents, discover MCP servers
• Brief confirmation: Write/update files (single batch yes/no)
• Ask first: git init, GitHub repo, delete existing content, major restructures

Reference Files

| When | Read | |------|------| | Building permission presets | [references/permission-presets.md](references/permission-presets.md) | | Generating CLAUDE.md, .gitignore | [references/templates.md](references/templates.md) | | Scoring CLAUDE.md quality | [references/quality-criteria.md](references/quality-criteria.md) | | Detecting project type + expected docs | [references/project-types.md](references/project-types.md) | | Setting up commit capture hook | [references/commit-hook.md](references/commit-hook.md) |