agent-doctor 🩺

Semantic health check for AI agent instruction files. Finds the instructions that will silently break your agent — before your agent runs.

The Problem

Structural linters check if your CLAUDE.md is well-formed. agent-doctor checks if it will actually work.

There's a difference.

# These pass every structural linter. They will break your agent.

- Be helpful and concise                          ← no decision boundary
- Always ask before making changes                ← conflicts with rule below
- Complete tasks autonomously without interruption ← decision loop on file edits
- Use the fetch_data tool to retrieve information  ← tool also writes logs (agent won't know)
- TODO: add more constraints here                  ← agent follows this literally

No regex catches these. No schema validates them. They require semantic reasoning — understanding what the agent will do with each instruction.

agent-doctor uses Claude (or OpenAI) to evaluate your instructions the way your agent will read them.

Quickstart

# Structural only — no API key needed
npx @chiragdarji/agent-doctor CLAUDE.md --structural-only

# Full analysis with Claude
ANTHROPIC_API_KEY=sk-ant-... npx @chiragdarji/agent-doctor CLAUDE.md

# Full analysis with OpenAI
OPENAI_API_KEY=sk-... npx @chiragdarji/agent-doctor CLAUDE.md --model gpt-4o

# Full analysis with Ollama (no cloud API key)
npx @chiragdarji/agent-doctor CLAUDE.md  # set provider/baseURL in .agentdoctor.json

# Auto-fix structural issues in-place
npx @chiragdarji/agent-doctor CLAUDE.md --fix

# Preview fixes without writing
npx @chiragdarji/agent-doctor CLAUDE.md --fix --dry-run

# Analyse all instruction files in the project
npx @chiragdarji/agent-doctor --all

# Run as MCP server (Claude Code / Cursor)
npx @chiragdarji/agent-doctor --mcp

Example Output

agent-doctor 🩺  Analysing CLAUDE.md...

❌  CRITICAL  Incomplete instruction marker "TODO" found
    Line 14: "TODO: add tool constraints here"
    Agent will follow this literally — replace before deploying.
    → Replace the placeholder with the actual instruction.

❌  CRITICAL  Unclosed code fence (```) — everything after line 22 is treated as code
    → Add a closing ``` fence to end the code block.

⚠   WARNING   Heading "Rules" appears more than once (lines 8 and 34)
    → Rename or merge — agents cannot determine which copy takes precedence.

⚠   WARNING   Rule 8 × Rule 12 — Decision loop detected
    Rule 8:  "Always ask before making file changes"
    Rule 12: "Complete tasks autonomously without interruption"
    → Add scope: "Ask only before destructive operations."

💡  SUGGEST   Section "Output Format" has >60% negation-based instructions
    → Rewrite as positive: "Never write long responses" → "Keep responses under 100 words"

────────────────────────────────────────────
Health Score  48 / 100  (D)
Issues        2 critical · 2 warnings · 1 suggestion
Files         CLAUDE.md
Model         claude-sonnet-4-6
────────────────────────────────────────────

What It Checks

agent-doctor runs two layers of analysis:

Layer 1 — Structural (13 rules, zero API cost)

| Rule | Severity | What it catches | |------|----------|----------------| | missing-frontmatter | critical | .mdc file missing --- YAML block | | unclosed-code-block | critical | Odd ``` fences — rest of file read as code | | todo-in-instructions | critical | TODO/FIXME/PLACEHOLDER left in — agent follows literally | | missing-always-apply | warning | .mdc where alwaysApply is not true | | missing-description | warning | .mdc with no description — Cursor can't match it contextually | | conflicting-frontmatter | warning | alwaysApply: true + globs set — globs silently ignored | | missing-file-glob | warning | alwaysApply: false + no globs — rule may never activate | | duplicate-heading | warning | Same heading twice — agent can't pick which wins | | legacy-format | warning | .cursorrules file ignored by agent mode | | token-budget-exceeded | warning | Section over configurable token threshold (default 500) | | empty-section | suggestion | Heading with no content and no children | | heading-depth-skip | suggestion | ## → #### jump — breaks hierarchy agents use for scoping | | negation-heavy | suggestion | >60% "don't/never/avoid" bullets — rewrite as positive |

Layer 2 — Semantic (8 rules, LLM-powered)

| Rule | Severity | What it catches | |------|----------|----------------| | decision-loop | critical | Two rules that conflict on a common task | | contradiction | critical | Rules that directly oppose each other | | vague-boundary | warning | Instructions with no measurable success condition | | tool-mismatch | warning | Tool description doesn't match schema behaviour | | missing-fallback | warning | Conditional with no else/default branch | | scope-bleed | warning | Rule intended for one context leaks into all contexts | | over-permissive | warning | Tool granted with no usage constraint | | ambiguous-pronoun | suggestion | "it", "they", "this" with no clear referent |

Supported Files

| File | Tool | |------|------| | CLAUDE.md | Anthropic Claude Code | | AGENTS.md | OpenAI Codex CLI, universal | | .cursor/rules/*.mdc | Cursor IDE | | GEMINI.md | Google Gemini CLI | | .github/copilot-instructions.md | GitHub Copilot | | .claude/agents/*.md | Claude Code subagents | | .claude/commands/*.md | Claude Code slash commands |

MCP Integration

agent-doctor runs as an MCP server so you can call it from inside Claude Code or Cursor. Pass your API key directly as a tool input — no environment variables needed.

Setup

// .claude/settings.json
{
  "mcpServers": {
    "agent-doctor": {
      "command": "npx",
      "args": ["@chiragdarji/agent-doctor", "--mcp"]
    }
  }
}

Tool: analyse_agent_file

Runs structural + semantic analysis on any instruction file.

{
  "filePath": "CLAUDE.md",
  "layers": ["structural", "semantic"],
  "model": "claude-sonnet-4-6",
  "anthropicApiKey": "sk-ant-...",
  "openaiApiKey": "sk-..."
}

| Input | Type | Required | Description | |-------|------|----------|-------------| | filePath | string | ✅ | Path to the instruction file | | layers | array | — | ["structural","semantic"] (default: both) | | model | string | — | e.g. claude-sonnet-4-6, gpt-4o | | anthropicApiKey | string | — | Falls back to ANTHROPIC_API_KEY env var | | openaiApiKey | string | — | Falls back to OPENAI_API_KEY env var |

No API key? Omit anthropicApiKey/openaiApiKey and set layers: ["structural"] for free analysis.

Tool: suggest_fix

Returns a built-in fix suggestion + LLM-generated before/after rewrite for a specific rule.

{
  "filePath": "CLAUDE.md",
  "issueRuleId": "todo-in-instructions",
  "anthropicApiKey": "sk-ant-..."
}

| Input | Type | Required | Description | |-------|------|----------|-------------| | filePath | string | ✅ | Path to the instruction file | | issueRuleId | string | ✅ | Rule ID from analyse_agent_file output | | anthropicApiKey / openaiApiKey | string | — | Enables LLM-generated rewrite |

Configuration

// .agentdoctor.json
{
  "model": "claude-sonnet-4-6",
  "layers": ["structural", "semantic"],
  "rules": {
    "negation-heavy": "off",
    "heading-depth-skip": "off",
    "missing-always-apply": "off"
  },
  "tokenBudgetWarning": 500,
  "ignore": [".claude/agents/legacy-*.md"],
  "failOn": "critical"
}

Using OpenAI:

{
  "model": "gpt-4o",
  "provider": "openai"
}

Using Ollama or any local LLM (no cloud API key needed):

{
  "provider": "openai-compatible",
  "baseURL": "http://localhost:11434/v1",
  "model": "llama3.1",
  "layers": ["structural", "semantic"]
}

Requires Ollama running locally: ollama pull llama3.1. See examples/ollama-config.json for a ready-to-use config.

Provider selection (priority order):

1. provider field in config — explicit override
2. Model name prefix: gpt-*, o1-*, o3-*, o4-* → OpenAI; else → Anthropic
3. API key present: ANTHROPIC_API_KEY → Anthropic, OPENAI_API_KEY → OpenAI

CLI Reference

agent-doctor [file] [options]

Arguments:
  file                    Path to instruction file (auto-detects CLAUDE.md if omitted)

Options:
  --all                   Discover and analyse all instruction files in the project
  --structural-only       Skip semantic layer — no API key required
  --model <id>            Override LLM model (e.g. gpt-4o, claude-opus-4-5)
  --fail-on <severity>    Exit code 1 if issues at this level (default: critical)
  --format <format>       Output format: text | json (default: text)
  --fix                   Auto-fix structural issues in-place
  --dry-run               Preview --fix changes without writing to disk
  --mcp                   Start MCP server mode
  -V, --version           Show version number
  -h, --help              Show help

Exit codes: | Code | Meaning | |------|---------| | 0 | No issues at or above --fail-on threshold | | 1 | Issues found at or above threshold | | 2 | File not found / parse error |

CI / CD Integration

GitHub Actions

# .github/workflows/agent-doctor.yml
name: Agent Instructions Health Check

on: [push, pull_request]

jobs:
  agent-doctor:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: '20'
      - name: Structural check (no API key needed)
        run: npx @chiragdarji/agent-doctor --all --structural-only --fail-on warning
      - name: Semantic check (optional — needs API key)
        if: env.ANTHROPIC_API_KEY != ''
        run: npx @chiragdarji/agent-doctor --all --fail-on critical
        env:
          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}

JSON output for downstream processing

npx @chiragdarji/agent-doctor CLAUDE.md --format json \
  | jq '.issues[] | select(.severity == "critical")'

Programmatic API

npm install @chiragdarji/agent-doctor

Basic usage

import { analyse, loadConfig } from '@chiragdarji/agent-doctor';

const config = loadConfig(process.cwd());
const result = await analyse('./CLAUDE.md', config);

console.log(result.score);   // 0–100
console.log(result.grade);   // 'A' | 'B' | 'C' | 'D' | 'F'
console.log(result.issues);  // Issue[]

Structural-only (no API key)

import { analyse, DEFAULT_CONFIG } from '@chiragdarji/agent-doctor';

const result = await analyse('./CLAUDE.md', {
  ...DEFAULT_CONFIG,
  layers: ['structural'],
});

Inject a custom LLM client

import { analyseSemantics, createAnthropicClient, createOpenAIClient } from '@chiragdarji/agent-doctor';

// Anthropic
const client = createAnthropicClient(process.env.ANTHROPIC_API_KEY!);
// OpenAI
const client = createOpenAIClient(process.env.OPENAI_API_KEY!);

const issues = await analyseSemantics(content, filePath, config, client);

Silence specific rules

const config = {
  ...loadConfig(process.cwd()),
  rules: {
    'negation-heavy': 'off',
    'heading-depth-skip': 'off',
  },
  failOn: 'warning',
};

Result shape

interface AnalysisResult {
  file: string;
  score: number;          // 0–100
  grade: 'A' | 'B' | 'C' | 'D' | 'F';
  issues: Issue[];
  tokenCount: number;
  analysedAt: string;     // ISO timestamp
  layers: ('structural' | 'semantic')[];
}

interface Issue {
  ruleId: RuleId;
  severity: 'critical' | 'warning' | 'suggestion';
  message: string;
  suggestion: string;
  line?: number;
  context?: string;
  relatedLine?: number;
}

Adding a New Structural Rule

1. Create src/rules/structural/<rule-id>.ts:

import type { Issue, StructuralRule } from '../../types.js';

/** Detects ... */
export const myRule: StructuralRule = (content, filePath) => {
  return []; // return Issue[] to flag, [] to pass
};

2. Export from src/rules/structural/index.ts
3. Add to rules array in src/analyser/structural.ts
4. Add RuleId to src/types.ts
5. Add tests in tests/structural.test.ts

How It Works

Your CLAUDE.md / AGENTS.md / .mdc
      │
      ├─► Layer 1: Structural (13 rules, regex-based, zero API cost)
      │         ├─► Frontmatter validation (missing, conflicting, incomplete)
      │         ├─► Content quality (empty sections, duplicate headings, TODOs)
      │         ├─► Code fence integrity (unclosed blocks)
      │         └─► Token budget per section
      │
      └─► Layer 2: Semantic (8 rules, LLM-powered)
                ├─► Reads instructions as an agent would
                ├─► Detects conflicts, ambiguities, missing boundaries
                └─► Returns structured JSON → Zod-validated → formatted output

The semantic layer sends only your instruction file (never your codebase) to the LLM API. All analysis runs locally. Nothing is stored or cached.

Roadmap

• [x] CLI — npx @chiragdarji/agent-doctor <file>
• [x] Structural layer — 13 rules, zero API cost
• [x] Semantic layer — 8 rules, Claude + OpenAI
• [x] OpenAI support (gpt-4o, o1-*, o3-*, o4-*)
• [x] MCP server — analyse_agent_file + suggest_fix tools with API key injection
• [x] Programmatic API (analyse, analyseAll, discoverFiles)
• [x] CI/CD mode (exit codes 0/1/2)
• [x] --fix — auto-fix structural issues (todo-in-instructions, unclosed-code-block, empty-section)
• [x] --dry-run — preview fixes without writing
• [x] Ollama / local LLM support via provider: "openai-compatible" + baseURL
• [x] Cursor semantic skill (skills/cursor-semantic-analysis/SKILL.md)
• [ ] VS Code extension (inline diagnostics)
• [ ] Cross-file conflict detection (CLAUDE.md vs AGENTS.md)
• [ ] Rule packs: cursor-pack, claude-code-pack, langgraph-pack
• [ ] Watch mode (re-analyse on save)

Auto-Fix (--fix)

agent-doctor can repair common structural issues automatically:

# Fix issues in-place
npx @chiragdarji/agent-doctor CLAUDE.md --fix

# Preview changes before writing
npx @chiragdarji/agent-doctor CLAUDE.md --fix --dry-run

| Rule | Fix action | |------|-----------| | todo-in-instructions | Replaces TODO line with <!-- TODO removed by agent-doctor — replace with actual instruction --> | | unclosed-code-block | Appends closing ``` fence at end of file | | empty-section | Inserts _No content yet — add instructions here._ after the heading | | legacy-format | Skipped — prints rename instruction; file rename must be manual |

Cursor Integration

agent-doctor works inside Cursor as an MCP server. For semantic analysis without a separate API key, use the included skill that lets Cursor's own LLM apply agent-doctor's semantic rules.

Setup (Cursor MCP)

Copy examples/cursor-mcp.json to .cursor/mcp.json in your project:

{
  "mcpServers": {
    "agent-doctor": {
      "command": "npx",
      "args": ["@chiragdarji/agent-doctor", "--mcp"],
      "env": {}
    }
  }
}

Cursor Semantic Analysis Skill

When you don't have a separate Anthropic/OpenAI key, use the skill at skills/cursor-semantic-analysis/SKILL.md — Cursor's built-in LLM performs the semantic analysis guided by agent-doctor's 8 semantic rules.

1. Use agent-doctor MCP: structural analysis on CLAUDE.md
2. Read CLAUDE.md fully
3. Apply agent-doctor semantic rules (from skill)
4. Output findings with health score

Ollama / Local LLM Support

Run full semantic analysis with no cloud API key using Ollama or any OpenAI-compatible endpoint:

# 1. Start Ollama and pull a model
ollama pull llama3.1

# 2. Copy the example config
cp examples/ollama-config.json .agentdoctor.json

# 3. Run analysis
npx @chiragdarji/agent-doctor CLAUDE.md

.agentdoctor.json:

{
  "provider": "openai-compatible",
  "baseURL": "http://localhost:11434/v1",
  "model": "llama3.1",
  "layers": ["structural", "semantic"]
}

Works with any OpenAI-compatible server: Ollama, LM Studio, vLLM, llama.cpp.

Why Not cclint / cursor-doctor / AgentLinter?

Those tools validate structure. agent-doctor validates semantics. They're complementary:

cclint / cursor-doctor  →  "Is this file valid?"
agent-doctor            →  "Will this file work?"

Contributing

git clone https://github.com/chiragdarji/agent-doctor
cd agent-doctor
npm install
npm run test        # 213 tests
npm run dev         # watch mode

See CONTRIBUTING.md.

License

MIT © Chirag Darji

Built because every structural linter said my CLAUDE.md was valid. My agent disagreed.