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certctl/docs/README.md
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shankar0123 476022ca59 docs(b6): secret-custody reference + config-encryption upgrade runbook + private-key CI guard 
Closes acquisition-diligence Bundle 6 findings on secret custody, config
encryption, and local artifact hygiene. Source IDs: S6, R4, SEC-M2,
RT-M1, RT-M2, RT-L1.

Surgical closures (artifact-only audit-framed memos stay out of the
public repo per the Bundle 5 lesson):

R4 / RT-L1 — local EC private key artifact
  rm cmd/agent/mc-001.key (gitignored, never in git history, leftover
  from a 2025-era agent dev run on the operator's workstation).
  Added scripts/ci-guards/B6-no-private-keys-in-tree.sh that fails the
  build if any TRACKED non-test file contains a PEM private-key block,
  so the next attempt to commit similar material gets caught at CI.
  Allowlist: *_test.go (hermetic-test PEMs), examples/*.md (sample
  walkthroughs), internal/scep/intune/testdata/ (certificates, not
  keys).

RT-M1 — landing-page HSM implication
  certctl.io/index.html: 'their hardware' / 'your hardware' colloquial
  comparisons rephrased to 'their custody' / 'your servers'. The phrase
  'Your keys. Your hardware. Your data. Your terms.' becomes 'Your
  keys. Your servers. Your data. Your terms.' to remove any inferred
  HSM-backed key-storage claim. The technical disclosure now lives in
  docs/operator/secret-custody.md (linked below); the landing page no
  longer makes a claim it cannot back.

S6 + SEC-M2 + RT-M2 (composite documentation closure)
  Added docs/operator/secret-custody.md — public operator reference
  enumerating every secret material on the control plane and on
  agents:
    - Local CA private key (FileDriver, file-on-disk, heap-resident
      with the L-014 carve-out documented in
      internal/connector/issuer/local/local.go).
    - Agent ECDSA P-256 keys (file on agent host, never transmitted).
    - OIDC client secret (AES-256-GCM v3, PBKDF2 600k).
    - Session signing key (same encryption regime).
    - Break-glass credential (Argon2id, never encrypted).
    - API-key bearer tokens (SHA-256 hash only; plaintext shown once).
    - CSR private keys mid-issuance (agent memory only).
    - Issuer-connector backend secrets (encrypted_config column,
      fail-closed for source='database', plaintext-by-design for
      source='env' with rationale).
  The Env-seeded-vs-DB-seeded plaintext policy is explained in plain
  text so a buyer review can independently verify the startup guard at
  cmd/server/main.go:222-262 makes sense.

  Added docs/operator/runbooks/config-encryption-upgrade.md — the
  procedural arm: how to force v1/v2 -> v3 re-seal across the
  database, plus the passphrase-rotation order. Documents the
  AEAD-driven read fallback (v3 -> v2 -> v1) and the fact that
  re-sealing happens passively on UPDATE. Open roadmap item: a
  certctl admin reseal --all command (tracked in
  WORKSPACE-ROADMAP.md).

  Both docs wired into docs/README.md Operator + Runbooks tables.

Verification:
  rg -n 'CONFIG_ENCRYPTION|encrypt|v1|private key|HSM|PKCS11|mc-001.key|\.key|Local CA' \
     internal cmd docs .gitignore README.md   # ambient (no NEW leaks)
  find . -name '*.key' \
     -not -path './.git/*' -not -path './web/node_modules/*'   # empty
  git ls-files | xargs grep -lE 'BEGIN .* PRIVATE KEY' \
     | grep -vE '_test\.go$|^examples/|^internal/scep/intune/testdata/'   # empty
  bash scripts/ci-guards/B6-no-private-keys-in-tree.sh   # PASS
  bash scripts/ci-guards/G-3-env-docs-drift.sh           # PASS
  bash scripts/ci-guards/doc-rot-detector.sh             # PASS

Residual roadmap (deliberately deferred):
  - signer.PKCS11Driver (HSM-token-backed CA-key custody).
  - signer.CloudKMSDriver (AWS/GCP/Azure KMS-backed CA-key custody).
  - FIPS 140-3 mode for the whole control plane.
  - HSM-backed session signing key.
  - Built-in 'certctl admin reseal --all' command.
  All five tracked in WORKSPACE-ROADMAP.md, not retracted.
2026-05-13 01:48:40 +00:00

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# certctl Documentation
> Last reviewed: 2026-05-12
The full docs index, organized by audience. Pick the section that matches what you need to do; each link below opens a focused doc rather than a wall of text.
For the elevator pitch and quickstart commands, see the repo `README.md` at the root. For the marketing site, see [certctl.io](https://certctl.io).
---
## Getting Started
You're new to certctl, just cloned the repo, or want to understand what it does before installing.
| Doc | What it covers |
|---|---|
| [Concepts](getting-started/concepts.md) | TLS certificates explained for beginners — CAs, ACME, EST, private keys, the full glossary |
| [Quickstart](getting-started/quickstart.md) | Five-minute setup with Docker Compose, dashboard tour, API tour |
| [Examples](getting-started/examples.md) | Five turnkey scenarios — ACME+NGINX, wildcard DNS-01, private CA+Traefik, step-ca+HAProxy, multi-issuer |
| [Advanced demo](getting-started/advanced-demo.md) | End-to-end certificate lifecycle with technical depth at each step |
| [Why certctl](getting-started/why-certctl.md) | Positioning vs ACME clients, agent-based SaaS, enterprise platforms; when to look elsewhere |
## Reference
You're operating certctl in production or building integrations and need authoritative technical detail.
| Doc | What it covers |
|---|---|
| [Architecture](reference/architecture.md) | System design, data flow, security model, deployment topologies |
| [Profiles](reference/profiles.md) | CertificateProfile policy object — issuer wiring, EKUs, RequiresApproval gate (with profile-edit closure) |
| [API](reference/api.md) | OpenAPI 3.1 spec, integration patterns, client SDK generation |
| [CLI](reference/cli.md) | certctl-cli command reference and CI/CD integration patterns |
| [Configuration](reference/configuration.md) | `CERTCTL_*` environment variable reference (scheduler, rate limits, deploy verify, audit, agent) |
| [MCP server](reference/mcp.md) | Model Context Protocol integration for AI assistants |
| [Release verification](reference/release-verification.md) | Cosign / SLSA / SBOM verification procedure |
| [Intermediate CA hierarchy](reference/intermediate-ca-hierarchy.md) | Multi-level CA tree management — RFC 5280 §3.2/§4.2.1.9/§4.2.1.10 enforcement |
| [Auth standards implemented](reference/auth-standards-implemented.md) | RFC + CWE evidence for the API-key + RBAC + OIDC + sessions + break-glass surface (NOT a compliance-mapping doc) |
| [Deployment model](reference/deployment-model.md) | Atomic write, post-deploy verify, rollback semantics across all targets |
| [Vendor matrix](reference/vendor-matrix.md) | Tested vendor versions per target connector |
### Connectors
The [connector index](reference/connectors/index.md) is the canonical catalog (interfaces, registry, scanners, plus an inline reference per built-in). Per-connector deep-dive siblings cover operator-grade material — vendor edges, troubleshooting, rotation playbooks, when-to-use vs alternatives.
**Issuers** (13 deep-dives): [ACME](reference/connectors/acme.md) · [ADCS](reference/connectors/adcs.md) · [AWS ACM Private CA](reference/connectors/aws-acm-pca.md) · [DigiCert](reference/connectors/digicert.md) · [EJBCA / Keyfactor](reference/connectors/ejbca.md) · [Entrust](reference/connectors/entrust.md) · [GlobalSign Atlas HVCA](reference/connectors/globalsign.md) · [Google CAS](reference/connectors/google-cas.md) · [Local CA](reference/connectors/local-ca.md) · [OpenSSL / Custom CA](reference/connectors/openssl.md) · [Sectigo SCM](reference/connectors/sectigo.md) · [step-ca / Smallstep](reference/connectors/step-ca.md) · [Vault PKI](reference/connectors/vault.md)
**Targets** (15 deep-dives): [Apache](reference/connectors/apache.md) · [AWS Certificate Manager](reference/connectors/aws-acm.md) · [Azure Key Vault](reference/connectors/azure-kv.md) · [Caddy](reference/connectors/caddy.md) · [Envoy](reference/connectors/envoy.md) · [F5 BIG-IP](reference/connectors/f5.md) · [HAProxy](reference/connectors/haproxy.md) · [IIS](reference/connectors/iis.md) · [Java Keystore](reference/connectors/jks.md) · [Kubernetes Secrets](reference/connectors/k8s.md) · [NGINX](reference/connectors/nginx.md) · [Postfix / Dovecot](reference/connectors/postfix.md) · [SSH (agentless)](reference/connectors/ssh.md) · [Traefik](reference/connectors/traefik.md) · [Windows Certificate Store](reference/connectors/wincertstore.md)
### Protocols
| Doc | What it covers |
|---|---|
| [ACME server](reference/protocols/acme-server.md) | Run certctl as an RFC 8555 + RFC 9773 ARI ACME server |
| [ACME server threat model](reference/protocols/acme-server-threat-model.md) | Security posture for the ACME server endpoint |
| [SCEP server](reference/protocols/scep-server.md) | RFC 8894 native SCEP server — RA cert config, multi-profile dispatch, must-staple, mTLS sibling route |
| [SCEP for Microsoft Intune](reference/protocols/scep-intune.md) | Intune-specific deployment guide — NDES replacement playbook |
| [EST server](reference/protocols/est.md) | RFC 7030 EST server — 802.1X / Wi-Fi enrollment, IoT bootstrap, channel binding |
| [CRL & OCSP](reference/protocols/crl-ocsp.md) | RFC 5280 CRL + RFC 6960 OCSP responder for relying parties |
| [Async CA polling](reference/protocols/async-ca-polling.md) | Bounded polling for async-CA issuer connectors |
## Operator
You're running certctl in production and need operational guidance.
| Doc | What it covers |
|---|---|
| [Security posture](operator/security.md) | Auth, rate limits, encryption at rest, key rotation, RBAC + OIDC + sessions + break-glass, bootstrap |
| [Secret custody](operator/secret-custody.md) | Where private keys live; FileDriver vs HSM/KMS; encryption wire format; env-seeded vs DB-seeded plaintext policy |
| [RBAC operator reference](operator/rbac.md) | Roles, permissions, scopes, scope-down + day-0 bootstrap |
| [Auth threat model](operator/auth-threat-model.md) | API-key + RBAC + OIDC + sessions + break-glass — token forgery, session hijacking, IdP compromise, role-grant abuse, bootstrap-token leak, audit-mutation |
| [OIDC / SSO runbooks](operator/oidc-runbooks/index.md) | Per-IdP setup guides — Keycloak, Authentik, Okta, Auth0, Entra ID, Google Workspace |
| [Control plane TLS](operator/tls.md) | Self-signed bootstrap, operator-supplied Secret, cert-manager Certificate CR |
| [Database TLS](operator/database-tls.md) | PostgreSQL transport encryption |
| [Approval workflow](operator/approval-workflow.md) | Two-person integrity gate for high-stakes issuance + profile-edit closure |
| [Helm deployment](operator/helm-deployment.md) | Kubernetes installation via the bundled chart |
| [Performance baselines](operator/performance-baselines.md) | Operator-runnable benchmarks for regression spot checks |
| [Auth benchmarks](operator/auth-benchmarks.md) | Session + OIDC validation p99 targets and measured baselines |
| [Legacy clients (TLS 1.2)](operator/legacy-clients-tls-1.2.md) | Reverse-proxy runbook for embedded EST/SCEP clients on TLS 1.2 |
### Runbooks
| Runbook | When |
|---|---|
| [Cloud targets](operator/runbooks/cloud-targets.md) | AWS ACM + Azure Key Vault deployment, debugging, rollback |
| [Expiry alerts](operator/runbooks/expiry-alerts.md) | Per-policy multi-channel routing matrix, severity tiers |
| [Disaster recovery](operator/runbooks/disaster-recovery.md) | CRL cache, OCSP responder cert, CA private-key rotation, Postgres restore |
| [Config-encryption upgrade](operator/runbooks/config-encryption-upgrade.md) | Force v1/v2 → v3 re-seal across the database; passphrase rotation procedure |
## Migration
You're moving from another cert-management tool to certctl, or running both in parallel.
| From | Doc |
|---|---|
| Certbot | [migration/from-certbot.md](migration/from-certbot.md) |
| acme.sh | [migration/from-acmesh.md](migration/from-acmesh.md) |
| cert-manager (coexistence, not replacement) | [migration/cert-manager-coexistence.md](migration/cert-manager-coexistence.md) |
| Caddy ACME (point Caddy at certctl) | [migration/acme-from-caddy.md](migration/acme-from-caddy.md) |
| cert-manager ACME (point cert-manager at certctl) | [migration/acme-from-cert-manager.md](migration/acme-from-cert-manager.md) |
| Traefik ACME (point Traefik at certctl) | [migration/acme-from-traefik.md](migration/acme-from-traefik.md) |
| **API keys → RBAC (v2.0.x → v2.1.0)** | [migration/api-keys-to-rbac.md](migration/api-keys-to-rbac.md) — **AUDIT YOUR API KEYS** post-upgrade |
| **Enable OIDC SSO** | [migration/oidc-enable.md](migration/oidc-enable.md) — step-by-step OIDC onboarding for an existing API-key + RBAC deployment |
## Contributor
You're contributing to certctl, running tests locally, or trying to understand the CI pipeline.
| Doc | What it covers |
|---|---|
| [Testing strategy](contributor/testing-strategy.md) | What we test and why; per-PR fast gates vs daily deep-scan |
| [Test environment](contributor/test-environment.md) | Local environment with real CAs (Pebble, step-ca, etc.) |
| [QA prerequisites](contributor/qa-prerequisites.md) | Before running QA: stack boot, demo data baseline, env vars |
| [QA test suite](contributor/qa-test-suite.md) | qa_test.go reference for release QA |
| [GUI QA checklist](contributor/gui-qa-checklist.md) | Manual GUI verification pass for release |
| [Release sign-off](contributor/release-sign-off.md) | Release-day checklist — code state, automated gates, manual QA, artefact verification |
| [CI pipeline](contributor/ci-pipeline.md) | CI shape, regression guards, adding new checks |
| [CI guards](contributor/ci-guards.md) | Per-class CI guards (code-shape, contract-parity, build/dep, operational); how to add one |
## Archive
Historical docs preserved for reference. Most operators don't need these.
| Doc | Why archived |
|---|---|
| [Upgrade to TLS (v2.2)](archive/upgrades/to-tls-v2.2.md) | Pre-v2.2 HTTPS-everywhere upgrade procedure |
| [Upgrade past v2 JWT removal](archive/upgrades/to-v2-jwt-removal.md) | G-1 milestone JWT auth removal procedure |
---
## Reading order by role
**First-time operator:** [Concepts](getting-started/concepts.md) → [Quickstart](getting-started/quickstart.md) → [Examples](getting-started/examples.md). About 90 minutes end to end.
**Production operator:** [Architecture](reference/architecture.md) → [Security posture](operator/security.md) → [Control plane TLS](operator/tls.md) → [Disaster recovery runbook](operator/runbooks/disaster-recovery.md). About 4 hours end to end.
**PKI engineer:** [ACME server](reference/protocols/acme-server.md) → [SCEP server](reference/protocols/scep-server.md) → [EST server](reference/protocols/est.md) → [Intermediate CA hierarchy](reference/intermediate-ca-hierarchy.md). About 6 hours end to end.
**Contributor:** [Architecture](reference/architecture.md) → [Testing strategy](contributor/testing-strategy.md) → [Test environment](contributor/test-environment.md) → [CI pipeline](contributor/ci-pipeline.md). About 3 hours end to end.
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