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docs: Phase 2 mechanical file moves to subdirectory structure

Browse Source 
Pure git mv operations; no content edits. Internal links remain pointing
at old paths and will be fixed in Phase 11. Per the Phase 1 audit
recommendations at cowork/docs-overhaul-phase-1-audit-2026-05-04/.

35 files moved across 8 audience-organized subdirectories:

  docs/getting-started/ (5):
    quickstart.md, concepts.md, examples.md, advanced-demo.md (was
    demo-advanced.md), why-certctl.md

  docs/reference/ (6):
    architecture.md, api.md (was openapi.md), mcp.md,
    intermediate-ca-hierarchy.md, deployment-model.md (was
    deployment-atomicity.md), vendor-matrix.md (was
    deployment-vendor-matrix.md)

  docs/reference/protocols/ (6):
    acme-server.md, acme-server-threat-model.md, scep-intune.md,
    est.md, crl-ocsp.md, async-ca-polling.md (was async-polling.md)

  docs/operator/ (4):
    security.md, tls.md, database-tls.md, approval-workflow.md

  docs/operator/runbooks/ (3):
    cloud-targets.md (was runbook-cloud-targets.md), expiry-alerts.md
    (was runbook-expiry-alerts.md), disaster-recovery.md

  docs/migration/ (3):
    from-certbot.md (was migrate-from-certbot.md), from-acmesh.md
    (was migrate-from-acmesh.md), cert-manager-coexistence.md (was
    certctl-for-cert-manager-users.md)

  docs/compliance/ (4):
    index.md (was compliance.md), soc2.md (was compliance-soc2.md),
    pci-dss.md (was compliance-pci-dss.md), nist-sp-800-57.md (was
    compliance-nist.md)

  docs/contributor/ (4):
    testing-strategy.md, test-environment.md (was test-env.md),
    ci-pipeline.md, qa-test-suite.md (was qa-test-guide.md)

Deferred to later Phase 2 sub-phases:
  - connectors.md split (Phase 4): docs/connectors.md +
    docs/connector-{apache,f5,iis,k8s,nginx}.md still at top level
  - testing-guide.md prune (Phase 5): docs/testing-guide.md still
    at top level
  - features.md disperse (Phase 6): docs/features.md still at top
    level
  - legacy-est-scep.md split (Phase 7): docs/legacy-est-scep.md
    still at top level
  - ACME walkthrough re-homing (Phase 8): three
    docs/acme-*-walkthrough.md still at top level
  - Upgrade docs archive (Phase 3): two docs/upgrade-*.md still
    at top level

Cross-reference updates (Phase 11) will happen after all moves and
content edits land. Internal links to docs/* paths are temporarily
broken until that phase completes.
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# MCP Server Guide
certctl ships with an MCP (Model Context Protocol) server that lets AI assistants manage your certificate infrastructure through natural language. Ask Claude to "show me all expiring certificates," "revoke the VPN cert," or "what agents are offline?" and the MCP server translates that into API calls against your certctl instance.
This guide covers setup, configuration, and usage with Claude, Cursor, and other MCP-compatible tools.
## What Is MCP?
MCP is an open protocol that connects AI assistants to external tools and data sources. Instead of copying and pasting API responses into a chat window, MCP lets the AI call your tools directly. The certctl MCP server exposes all 78 API endpoints as MCP tools — the AI sees typed schemas describing what each tool does, what parameters it accepts, and what it returns.
The MCP server is a separate binary (`cmd/mcp-server/`) that communicates via stdio transport. It's a stateless HTTP proxy: every MCP tool call becomes an HTTP request to the certctl REST API. No new state, no new database tables, no new attack surface beyond what the API already exposes.
## Prerequisites
You need:
1. A running certctl server (see [Quick Start](quickstart.md))
2. The MCP server binary — either built from source or from a Docker image
3. An MCP-compatible AI client (Claude Desktop, Cursor, VS Code with Copilot, etc.)
## Building the MCP Server
```bash
cd certctl
go build -o certctl-mcp ./cmd/mcp-server/
```
The binary has zero runtime dependencies beyond the certctl server it connects to.
## Configuration
The MCP server reads three environment variables:
| Variable | Required | Default | Description |
|----------|----------|---------|-------------|
| `CERTCTL_SERVER_URL` | No | `https://localhost:8443` | URL of the certctl REST API (HTTPS-only as of v2.2) |
| `CERTCTL_API_KEY` | No | (empty) | API key for authentication (passed as `Bearer` token) |
| `CERTCTL_SERVER_CA_BUNDLE_PATH` | Yes (for self-signed / internal CA) | (empty) | Path to PEM CA bundle that signed the server cert. Required when the server cert isn't rooted in the system trust store (the default compose stack ships a self-signed cert at `deploy/test/certs/ca.crt`). |
If your certctl server has auth enabled (the default), you must provide the API key. The MCP server passes it through to every HTTP request.
Since v2.2 the certctl control plane is HTTPS-only. If the server cert is self-signed or chained to an internal CA, set `CERTCTL_SERVER_CA_BUNDLE_PATH` so the MCP server can verify the TLS handshake. Never set `CERTCTL_SERVER_TLS_INSECURE_SKIP_VERIFY=true` outside local development — it disables all certificate validation.
## Setting Up with Claude Desktop
Add this to your Claude Desktop MCP configuration file (`~/Library/Application Support/Claude/claude_desktop_config.json` on macOS, `%APPDATA%\Claude\claude_desktop_config.json` on Windows):
```json
{
"mcpServers": {
"certctl": {
"command": "/path/to/certctl-mcp",
"env": {
"CERTCTL_SERVER_URL": "https://localhost:8443",
"CERTCTL_SERVER_CA_BUNDLE_PATH": "/path/to/certctl/deploy/test/certs/ca.crt",
"CERTCTL_API_KEY": "your-api-key-here"
}
}
}
}
```
Restart Claude Desktop. You should see "certctl" appear in the MCP tools list with 78 available tools.
## Setting Up with Cursor
In Cursor, go to Settings → MCP Servers and add:
```json
{
"certctl": {
"command": "/path/to/certctl-mcp",
"env": {
"CERTCTL_SERVER_URL": "https://localhost:8443",
"CERTCTL_SERVER_CA_BUNDLE_PATH": "/path/to/certctl/deploy/test/certs/ca.crt",
"CERTCTL_API_KEY": "your-api-key-here"
}
}
}
```
## Setting Up with Claude Code
Add certctl as an MCP server in your project's `.mcp.json`:
```json
{
"mcpServers": {
"certctl": {
"command": "/path/to/certctl-mcp",
"env": {
"CERTCTL_SERVER_URL": "https://localhost:8443",
"CERTCTL_SERVER_CA_BUNDLE_PATH": "/path/to/certctl/deploy/test/certs/ca.crt",
"CERTCTL_API_KEY": "your-api-key-here"
}
}
}
}
```
## Available Tools
The MCP server exposes the full REST API organized across 16 resource domains:
| Domain | Tools | Examples |
|--------|-------|---------|
| Certificates | 9 | List, get, create, update, archive, versions, renew, deploy, revoke |
| CRL & OCSP | 3 | Get JSON CRL, get DER CRL by issuer, check OCSP status |
| Issuers | 6 | List, get, create, update, delete, test connection |
| Targets | 5 | List, get, create, update, delete |
| Agents | 8 | List, get, register, heartbeat, CSR submit, certificate pickup, get work, report job status |
| Jobs | 5 | List, get, cancel, approve, reject |
| Policies | 6 | List, get, create, update, delete, list violations |
| Profiles | 5 | List, get, create, update, delete |
| Teams | 5 | List, get, create, update, delete |
| Owners | 5 | List, get, create, update, delete |
| Agent Groups | 6 | List, get, create, update, delete, list members |
| Audit | 2 | List events (with filters), get event by ID |
| Notifications | 3 | List, get, mark as read |
| Stats | 5 | Summary, certs by status, expiration timeline, job trends, issuance rate |
| Metrics | 1 | System metrics (gauges, counters, uptime) |
| Health | 4 | Health check, readiness probe, auth info, auth check |
Every tool has typed input parameters with `jsonschema` descriptions, so the AI knows exactly what arguments to provide and what each field means.
## Example Conversations
Once configured, you can interact with certctl through natural language:
**"Show me all certificates expiring in the next 14 days"**
The AI calls `certctl_list_certificates` with `status=Expiring` and interprets the results.
**"Renew the API production certificate"**
The AI calls `certctl_trigger_renewal` with `id=mc-api-prod`.
**"Who owns the payments gateway cert?"**
The AI calls `certctl_get_certificate` with `id=mc-payments-prod` and reads the `owner_id` and `team_id` fields.
**"Are any agents offline?"**
The AI calls `certctl_list_agents` and checks the heartbeat timestamps.
**"Revoke the old VPN cert — the key was compromised"**
The AI calls `certctl_revoke_certificate` with `id=mc-vpn-old` and `reason=keyCompromise`.
**"Give me a summary of the certificate fleet"**
The AI calls `certctl_dashboard_summary` for aggregate stats, then optionally `certctl_certificates_by_status` for the breakdown.
**"Create a new cert for staging.api.example.com owned by the platform team"**
The AI calls `certctl_create_certificate` with the common name, team ID, and owner ID.
## Architecture
```mermaid
flowchart LR
AI["AI Assistant\n(Claude, Cursor)"]
MCP["certctl MCP\ncmd/mcp-server/"]
SERVER["certctl Server\n:8443"]
AI <-->|"stdio"| MCP
MCP -->|"HTTP + Bearer token"| SERVER
MCP ~~~ TOOLS["REST API via MCP · 16 domains\nTyped input structs"]
```
The MCP server is intentionally thin:
- **No state** — every request is a pass-through HTTP call. Restart it anytime.
- **No new auth** — uses the same API key as the REST API.
- **No new dependencies** — just the official MCP Go SDK (`modelcontextprotocol/go-sdk`).
- **No new attack surface** — the AI can only do what the API key allows.
## Security Considerations
The MCP server inherits the security properties of the REST API:
- **API key scoping**: The MCP server uses whatever API key you configure. If certctl gets API key scoping in a future release (per-resource or per-action permissions), the MCP server will automatically respect those restrictions.
- **Audit trail**: Every tool call results in an HTTP request that's logged in the API audit middleware — actor, method, path, status, and latency are all recorded.
- **Read-only usage**: For read-only AI access, you could configure a restricted API key (when key scoping ships). Until then, be aware that the AI can call write endpoints (create, update, delete, revoke) if the API key permits it.
- **No private key exposure**: The MCP server never sees or transmits private keys — the same architectural guarantee as the REST API.
## Troubleshooting
**"MCP server not connecting"**
Check that `CERTCTL_SERVER_URL` is reachable from where the MCP binary runs. Try `curl $CERTCTL_SERVER_URL/health` to verify.
**"401 Unauthorized on every tool call"**
Your `CERTCTL_API_KEY` is missing or wrong. Check the key matches what the certctl server expects.
**"Tool calls return empty results"**
The certctl server might have no data. Run the demo seed (`docker compose up`) to populate demo data, or check that your database has records.
## What's Next
- [Quick Start](quickstart.md) — Get certctl running locally
- [OpenAPI Spec](openapi.md) — Full API reference and SDK generation
- [Architecture](architecture.md) — System design deep dive
- [Concepts](concepts.md) — Certificate lifecycle fundamentals