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jakman85andClaude Opus 5 b7341b329b fix(runbooks): declare whole-repo scope, drop the bespoke l0 stage, +cnpg-primary-spread

Three corrections after rebasing onto main.

1. THE GUARD CAUGHT A REAL ONE ON ITS FIRST CONTACT WITH main. main had gained
   `CNPGPrimariesCoLocated` (platform/cnpg/alerts.yaml) pointing at
   /runbooks/cnpg-primary-spread, with no runbook. The check failed the rebase exactly as
   designed — 46 annotations, 35 names, 34 present — naming both the missing file AND the
   missing configMapGenerator entry. runbooks/cnpg-primary-spread.md now exists: what
   co-located primaries actually cost here (blast radius, not an outage, because
   instances: 3 + required anti-affinity), why the drift is uncorrectable-by-declaration
   (CNPG has no primary-placement field), the readiness gate that keeps the rule quiet
   during a real node outage, and the ~9s-per-database switchover rebalance, one cluster
   at a time. The 2026-09-07 outage in which all three primaries sat on one node is the
   reason the alert exists at all.

2. WHOLE-REPO SCOPE, NOT A HAND-WRITTEN STAGE. main's refactor replaced ci/l0.sh's
   per-check "UNCONDITIONAL" stages with a declaration:
   `conformance.home.k3s/scope: "whole-repo"`, unioned into every gate run by Stage 3b's
   `--include-scope`. My +38-line Stage 3f is removed (ci/l0.sh is now byte-identical to
   main) and the annotation is declared instead. Assertion (7) of the check was rewritten
   to match: it no longer asserts its own path appears in ci/l0.sh — it asserts the test
   DECLARES the scope and that ci/l0.sh still passes --include-scope, since neither half
   alone makes the check load-bearing. That matters here because
   ci/touched-requirements.sh maps platform/monitoring/* to "R-OBS-01 R-OBS-02", not
   R-OBS-04, and maps platform/kubevirt/* and runbooks/* to nothing at all.

3. A FACTUAL CORRECTION IN ALL 35 RUNBOOKS. Every page claimed `dev.sh` defaults its
   current-context to k3s-dev. main's `9b4744d fix(devcontainer): dev.sh defaults to
   prod` made that false, and a runbook that misstates which cluster a command talks to is
   worse than one that says nothing. The pages now say what is durably true: the default
   has already changed once, so naming `--context k3s-prod` is what makes a command mean
   the same thing next month, and the per-invocation banner is there to be read. The
   check's own failure message was corrected the same way.

Re-verified after all three: check green at 374 assertions (46 annotations, 35/35 runbooks
present, 35/35 projected), re-applied to prod, and re-probed in-cluster through the
Gateway — node-down, keycloak-down, keycloak-client-secrets, cnpg-archiving,
longhorn-faulted, vpn-down, node-io and cnpg-primary-spread all HTTP 200 with
text/plain; charset=utf-8 and 8.9-12.1 KB of real body; /runbooks/ index 200; an unknown
name 404s with a pointer rather than a blank page; and homepage still answers the apex `/`,
confirming Gateway API longest-path precedence.

Full merge gate: PASS (spec-immutability, lint, l0, render-golden, l1 all green;
prom-rules SKIPPED for want of promtool in the image; L2/L3 SKIPPED, no cluster).

Co-Authored-By: Claude Opus 5 <[email protected]>

2026-09-13 00:00:24 -05:00

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backup-partial — A Velero backup completed with partial failures

Alert: VeleroBackupPartialFailure (warning, 5m) File: platform/monitoring/alerts.yaml, group platform-health.backups Expression: increase(velero_backup_partial_failure_total[1h]) > 0

What this means here

The backup finished, but some resources or volumes were skipped or errored. It is a warning rather than a critical because most of it worked — and that is exactly what makes it dangerous: a PartiallyFailed backup looks like a backup in every listing, and the thing it silently omitted may be the thing you need.

The first question is always: was the skip deliberate? On this cluster a great deal of skipping is intentional and correct.

READ THIS BEFORE YOU CONCLUDE THE BACKUPS ARE GONE

kubectl get backup -A prints "No resources found" on this cluster even when backups exist. Three CRDs register the kind Backup — longhorn.io/v1beta2, postgresql.cnpg.io/v1 and velero.io/v1 — and the bare short name resolves to Longhorn's, which holds zero objects. Verified on prod 2026-09-13: the fully-qualified queries returned 6 Velero backups and 27 CNPG backups while the short name returned nothing. This false negative has already produced two wrong "the backups are missing" conclusions in one night. A destructive recovery action taken on it is how a CLI quirk becomes real data loss. Always:

backups.velero.io           backups.postgresql.cnpg.io           backups.longhorn.io
schedules.velero.io         scheduledbackups.postgresql.cnpg.io  clusters.postgresql.cnpg.io

The deliberate exclusions (know these before calling anything a failure)

NFS-sourced volumes are skipped on purpose, and the reason is a near-miss worth remembering. The opt-out file-system-backup schedule (defaultVolumesToFsBackup: true, excluding only monitoring and unifi) would have read the NFS media library three times — plex-media, sonarr-media and radarr-media are all bound to the same 192.168.2.102:/mnt/Storage/plex export, 8.32 TiB measured — plus nextcloud-legacy-archive (270 GiB), pushing roughly 8.6 TiB to R2 nightly with 720h retention. Namespace exclusion could not express the fix, because those namespaces also hold real Longhorn PVCs that must be backed up.

The fix is a per-volume opt-out by SOURCE TYPE: the ConfigMap velero-volume-policies skips any volume whose source is NFS, and the schedule references it. The per-pod backup-volumes-excludes annotation was rejected for failing OPEN (forget the annotation and you back up 8 TiB). Proven on prod: a Backup of namespace nextcloud produced exactly one PodVolumeBackup (data, Longhorn, 875,417,102 bytes, Completed) and the NFS volume produced none. Residual gap, stated honestly: the rule matches NFS only. A future non-NFS bulk source would not be covered.

The three CNPG databases are also out of scope by design. keycloak-db, nextcloud-db and semaphore-db have their own DR path (Barman WAL archive + base backups to R2) because a Velero snapshot of a live Postgres is not a backup. If a *-db-N volume is skipped, that is correct — see /runbooks/cnpg-archiving for the path that does cover them.

monitoring and unifi are excluded from file-system backup as well.

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 (git push origin main is the deploy). Where this runbook gives a mutating command it is for an operator, and it says so.

First commands

Which backup, and what exactly it warned about:

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod get backups.velero.io -A \
     -o custom-columns=NAME:.metadata.name,PHASE:.status.phase,ERRORS:.status.errors,WARN:.status.warnings,START:.status.startTimestamp'

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod -n velero get backups.velero.io <name> -o yaml | sed -n "/status:/,\$p"'

Per-volume results — this tells you whether a skip was the NFS policy or a real failure:

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod -n velero get podvolumebackups.velero.io \
     -o custom-columns=NAME:.metadata.name,BACKUP:.metadata.labels.velero\\.io/backup-name,POD:.spec.pod.name,VOL:.spec.volume,PHASE:.status.phase,BYTES:.status.progress.bytesDone'

The volume policy that does the deliberate skipping:

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod -n velero get cm velero-volume-policies -o yaml'

The controller's own account of what it skipped:

infra/devcontainer/dev.sh run bash -c \
  'kubectl --context k3s-prod -n velero logs deploy/velero --tail=200 2>&1 | grep -iE "skip|excluded|warn|error" | tail -30'

Likely causes, most likely first

1. The deliberate NFS / CNPG / monitoring exclusions

Most common by far, and correct. Confirm against the velero-volume-policies ConfigMap and the schedule's excluded namespaces. No action. If you are tempted to "fix" it, re-read the 8.6 TiB near-miss above.

2. A resource Velero could not serialise

Usually a CRD whose API was unavailable at the moment of the backup, or an admission webhook refusing a read. The log names the group/kind. Often transient; if it recurs for the same kind, that kind is genuinely not backed up.

3. A volume was busy, degraded, or on a node under pressure

Velero's daily runs at 03:00 against Longhorn PVCs. A degraded volume or a node with high I/O-PSI can fail one volume's read while the rest succeed. Cross-read /runbooks/longhorn-degraded and /runbooks/node-io.

4. A partial R2 write

Related to the tagging/checksum incompatibilities in /runbooks/backup-failure: those normally produce a hard Failed, but a partially-written backup is worth checking the plugin pin for (velero/velero-plugin-for-aws:v1.14.3-rc.2 — do not revert to v1.14.2).

5. A namespace was created or deleted mid-backup

Benign race. Leaked test namespaces have existed on this cluster and been deleted; a namespace disappearing under Velero produces exactly this warning.

When to escalate or stop

Decide, and record, whether the skipped items matter. The honest failure mode here is shrugging at a PartiallyFailed and discovering later that something was never covered. If the skip was not one of the documented exclusions, treat it as an uncovered resource.
Do not add namespaces to the exclusion list to quiet the alert. Those namespaces hold real Longhorn PVCs; namespace-level exclusion is the mistake the source-type policy exists to avoid.
Do not switch to the per-pod backup-volumes-excludes annotation — it was rejected for failing OPEN, and the consequence of forgetting it is 8 TiB per night.
Do not delete a PartiallyFailed backup — like a Failed one it can leave orphaned kopia blobs, and deleting R2 objects is an operator decision.
Escalate if the same resource or volume is skipped on consecutive nights: that is a coverage gap, which is an R-STATE-03 matter and not a transient.

Source of truth: runbooks/backup-partial.md. Index: /runbooks/ Records: commit 2e259a8 (the 8.6 TiB near-miss, the source-type volume policy, and the rejection of the fail-open annotation); docs/BULK-NFS-STORAGE.md.

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