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-<!--
-Placeholder for the docs/ navigation index.
-
-Populated in Phase 12 of the docs overhaul restructure (see
-cowork/docs-overhaul-phase-2-restructure-prompt.md). Will become the
-audience-organized index linking into the eight subdirectories under
-docs/: getting-started, reference, operator, migration, compliance,
-contributor, archive.
-
-Subdirectory population begins in Phase 2 (file moves).
--->
-
 # certctl Documentation
 
 > Last reviewed: 2026-05-05
 
-This index is being rebuilt as part of the Phase 2 documentation
-restructure. See `cowork/docs-overhaul-phase-2-restructure-prompt.md`
-for the plan and `README.md` (root) for the current operator entry
-point until this index lands.
+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 |
+| [API](reference/api.md) | OpenAPI 3.1 spec, integration patterns, client SDK generation |
+| [MCP server](reference/mcp.md) | Model Context Protocol integration for AI assistants |
+| [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 |
+| [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
+
+| Doc | What it covers |
+|---|---|
+| [Connector index](reference/connectors/index.md) | Issuer/target/notifier interface contracts, registry, scanners |
+| [Apache](reference/connectors/apache.md) | Apache httpd connector deep dive |
+| [F5 BIG-IP](reference/connectors/f5.md) | F5 connector — proxy agent + transactional iControl REST |
+| [IIS](reference/connectors/iis.md) | Microsoft IIS — local PowerShell + WinRM modes |
+| [Kubernetes Secrets](reference/connectors/k8s.md) | Kubernetes Secrets connector |
+| [NGINX](reference/connectors/nginx.md) | NGINX connector — deploy contract + quirks |
+
+### 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 |
+| [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 |
+| [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 |
+
+## 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) |
+
+## Compliance
+
+You're working through a SOC 2, PCI, or NIST audit and need to map certctl's capabilities to control objectives.
+
+| Doc | What it covers |
+|---|---|
+| [Compliance overview](compliance/index.md) | What these guides cover and what they don't |
+| [SOC 2 Type II](compliance/soc2.md) | Trust Service Criteria mapping (CC6, CC7, CC8, A1) |
+| [PCI-DSS 4.0](compliance/pci-dss.md) | Requirements 3, 4, 6, 7, 8, 10 |
+| [NIST SP 800-57](compliance/nist-sp-800-57.md) | Key management alignment with NIST guidance |
+
+## 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 test suite](contributor/qa-test-suite.md) | qa_test.go reference for release QA |
+| [CI pipeline](contributor/ci-pipeline.md) | CI shape, regression guards, adding new checks |
+
+## 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.
+
+**Auditor / compliance team:** [Compliance overview](compliance/index.md) → applicable framework doc → [Disaster recovery runbook](operator/runbooks/disaster-recovery.md) → [Approval workflow](operator/approval-workflow.md) → [ACME server threat model](reference/protocols/acme-server-threat-model.md). About 4 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.