home-network-k3s-impl/runbooks/cert-issuance.md

cert-issuance — A Certificate is not Ready (ACME issuance is failing)

Alert: CertificateNotReady (warning, 1h) File: platform/monitoring/alerts.yaml, group platform-health.certificates Expression: certmanager_certificate_ready_status{condition="False"} == 1

What this means here

cert-manager cannot issue or renew a certificate. The one that matters is wildcard-home in the gateway namespace — secret wildcard-home-tls, requesting both *.${BASE_DOMAIN} and ${BASE_DOMAIN} from ${ACME_CLUSTER_ISSUER} (letsencrypt-prod on prod). Every HTTPS listener on the shared Gateway terminates with it, so issuance failing is a slow-burning cluster-wide outage: it does nothing today and takes down every hostname plus in-cluster SSO when the existing certificate expires. The 1h for reflects that — a failing order is worth investigating today, not paging at 3am.

The solver is DNS-01 against Cloudflare, which matters because DNS-01 has a failure mode this cluster has already hit:

The self-check, not the challenge, is the usual failure. On 2026-08-16 the wildcard stalled with the challenge at Presented=true — the Cloudflare TXT record was created, so the API token worked — while cert-manager's propagation self-check looped "DNS record not yet propagated". The record was publicly resolvable at 1.1.1.1 and 8.8.8.8; the NAT'd cluster's own DNS could not see it, because split-horizon CoreDNS answers authoritatively for the zone and never forwards. The fix is live in platform/cert-manager/helmrelease.yaml:

dns01RecursiveNameservers: "1.1.1.1:53,8.8.8.8:53"
dns01RecursiveNameserversOnly: true

The challenge went pending → valid and the certificate Issued. If you find those two lines missing or changed, that is your answer.

Verify the alert can even fire (measured 2026-09-13)

This alert is currently INERT. count(certmanager_clock_time_seconds) returned 0 series on prod — there is no cert-manager scrape job among Prometheus's 19 jobs, so all three certificate rules evaluate against nothing. Certificate health must be read from the CRs, as below. See /runbooks/targets-down for the full list of inert rule groups.

Running the commands in this runbook

kubectl does not work on the operator workstation. The toolchain lives only in the pinned dev container, and the host's k3s-oidc context hangs on a browser prompt once its token expires — that hang is not the cluster being down. Every command below runs as:

infra/devcontainer/dev.sh run bash -c 'kubectl --context k3s-prod get nodes'

Always pass --context k3s-prod explicitly. dev.sh merges BOTH clusters into one kubeconfig and picks a current-context per invocation, and that default has already changed once — it was k3s-dev until dev was decommissioned on 2026-09-13, and is k3s-prod now. A command that names its context means the same thing next month as it does today; one that relies on the default does not, and the failure is silent (it answers confidently about the other cluster). CLUSTER=prod infra/devcontainer/dev.sh run kubectl ... selects it explicitly, and every invocation prints a banner naming the cluster it is about to talk to — read it. Do not run two dev.sh invocations at once; they share one container and interfere.

USE FULLY-QUALIFIED RESOURCE NAMES, ALWAYS. Three CRDs on this cluster register the kind Backup: longhorn.io/v1beta2, postgresql.cnpg.io/v1 and velero.io/v1. The bare short name resolves to Longhorn's, which holds zero objects — so kubectl get backup -A prints "No resources found" on a cluster holding 6 Velero backups and 27 CNPG backups. Verified on prod 2026-09-13. Reading that as "the backups are gone" and acting on it turns a false negative into real data loss. Write backups.velero.io, backups.postgresql.cnpg.io, clusters.postgresql.cnpg.io, settings.longhorn.io, volumes.longhorn.io, nodes.longhorn.io.

Mutating kubectl (apply, patch, annotate, rollout) and flux reconcile are blocked for agents here: every durable change goes through git. main is a protected branch — a direct push is rejected. A change lands by pushing a branch, opening a PR, and merging it once the gate is green; that merge is the deploy. Where this runbook gives a mutating command it is for an operator, and it says so.

First commands

Walk the chain top-down — Certificate → CertificateRequest → Order → Challenge. The failure is almost always visible at one specific level:

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod get certificates.cert-manager.io -A \
     -o custom-columns=NS:.metadata.namespace,NAME:.metadata.name,READY:.status.conditions[?\(@.type==\"Ready\"\)].status,MSG:.status.conditions[?\(@.type==\"Ready\"\)].message,NOTAFTER:.status.notAfter'

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod get certificaterequests.cert-manager.io -A; echo ==; \
   kubectl --context k3s-prod get orders.acme.cert-manager.io -A; echo ==; \
   kubectl --context k3s-prod get challenges.acme.cert-manager.io -A -o wide'

The controller log, which carries the actual ACME error text:

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod -n cert-manager logs deploy/cert-manager --tail=150 2>&1 | grep -iE "error|propagat|challenge|order|rate" | tail -30'

Is the TXT record really there? Ask the authority, never a resolver — 1.1.1.1 has served a deleted TXT record here for minutes and produced a false failure diagnosis:

dig +short @betty.ns.cloudflare.com _acme-challenge.home.keithjackson.dev TXT
dig +short @1.1.1.1 _acme-challenge.home.keithjackson.dev TXT

Is the resolver override still configured?

grep -n "dns01Recursive" platform/cert-manager/helmrelease.yaml

The issuer and its credential:

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod get clusterissuers.cert-manager.io \
     -o custom-columns=NAME:.metadata.name,READY:.status.conditions[?\(@.type==\"Ready\"\)].status,MSG:.status.conditions[?\(@.type==\"Ready\"\)].message'

Likely causes, most likely first

1. The DNS-01 propagation self-check cannot resolve the TXT record

The recorded failure. Signature: Challenge Presented=true, status looping on "DNS record not yet propagated", and dig @betty.ns.cloudflare.com does return the TXT. Cause: cert-manager is asking the cluster's own resolver, which is split-horizon CoreDNS answering authoritatively for the zone and never forwarding. Remediation: the two dns01Recursive* values above, in git.

2. The Cloudflare API token is wrong, expired, or scoped too narrowly

Signature: Challenge never reaches Presented=true, and the log carries a Cloudflare 403/6003. The token lives in a SOPS-encrypted Secret. Note the standing rule from the OIDC incident: non-secret environment-specific values must never live inside an encrypted Secret — ${BASE_DOMAIN} substitution cannot reach inside one, and that is precisely how prod's OIDC clients once ended up pointed at dev's Keycloak. Keep hostnames out; keep only the token in.

3. EXTERNALDNS_DOMAIN_FILTER / zone confusion

Recorded as finding F-DNS1: the filter must be the ZONE (keithjackson.dev), not the subdomain. A zone mismatch means the TXT record is created in the wrong place or not at all.

4. Two clusters racing the same _acme-challenge record

infra/PROD-PROVISIONING.md §10: after the 2026-09-04 incident platform-config would have requested a *.home.keithjackson.dev wildcard from letsencrypt-prod for a certificate dev already held; both clusters would then have raced each other's _acme-challenge TXT records on one Cloudflare zone and neither would reliably solve DNS-01. Only the tier being suspended prevented it. If any second cluster exists, establish which one owns the zone first.

5. Let's Encrypt rate limit

too many certificates already issued in the log. One wildcard is well inside the limits, so this means something has been retrying in a loop. Stop the loop and wait out the window.

6. A new Certificate for a hostname that does not resolve

A newly added service whose DNS is not yet published cannot solve DNS-01. Check ExternalDNS first.

When to escalate or stop

• Escalate if wildcard-home has been not-Ready for more than a day, and check /runbooks/cert-expiry for how much runway the existing certificate has. Under 3 days of runway is an operator page.
• Never switch ${ACME_CLUSTER_ISSUER} to letsencrypt-staging to get a green certificate. Staging issues fine and then breaks every in-cluster OIDC client with x509: certificate signed by unknown authority — that is the bug that forced LE-prod in the first place.
• Do not delete the existing wildcard-home-tls Secret while issuance is broken. A stale but valid certificate is far better than none.
• Do not create certificates by hand. cert-manager owns them; the durable change is in git.
• Rotating the Cloudflare token is an operator action (SOPS, DR path).

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Source of truth: runbooks/cert-issuance.md. Index: /runbooks/ Records: DECISIONS-LOG.md "Fix 5 — cert-manager DNS-01 self-check via public resolvers" (commit ~59dd3d9) and the LE-staging → LE-prod switch; infra/PROD-PROVISIONING.md §10.