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jakman85andClaude Opus 5 f21e89d9d2

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fix(gitops): CDI cold-start deadlock repaired IN THE GRAPH, not by a pre-apply

`platform-config` applied the CDI CR *and* cdi-storageprofiles.yaml in ONE pass.
StorageProfile's CRD does not exist until cdi-operator reconciles that CR, and
Flux server-side dry-runs every object before applying any — so the unknown kind
aborted the tier, the CR was never applied, the CRD was never created, and the
tier could NEVER converge. Observed on prod: cdi-operator Available 12h, no CDI
CR, no storageprofiles CRD, every downstream tier blocked.

The profiles now live in their own tier ./platform-config-cdi with
dependsOn: platform-config and wait: true. Because dependsOn is REVISION-gated
and platform-config runs wait: true, the CDI CR must be applied AND healthy —
exactly the event that creates the CRD — before the profiles are applied. Cold
clusters order themselves. `standup.sh crds` is retained as a fallback for
clusters already stuck, and because it is idempotent.

THE GENERALISABLE RULE (recorded in clusters/README.md): a CR whose CRD is
created by a CONTROLLER AT RUNTIME is second-order and needs its own pass.
cdi-operator.yaml registers exactly ONE CRD (cdis.cdi.kubevirt.io); storageprofiles,
datavolumes, datasources and dataimportcrons appear only after it reconciles the
CDI CR. An audit found StorageProfile is the only second-order kind in
platform-config — KubeVirt, CDI, KeycloakRealmImport, CNPG Cluster,
VolumeSnapshotClass, ClusterIssuer, PrometheusRule, ServiceMonitor and the Cilium
L2 CRs all have their CRD in git or in a chart.

Moving the CDI CR up into `platform` was rejected: that would put CDI's health on
the tier the CNI gates and everything waits on — the mistake the oauth2-proxy and
headlamp splits exist to undo.

apps-vms gains dependsOn: platform-config-cdi. LOAD-BEARING, not cosmetic:
apps/vms/unifi/20-datavolume.yaml provisions on storageClassName: longhorn-vm and
its comment claimed platform-config guaranteed the profiles — which this move
would have silently falsified.

THE PRUNE TRANSIENT, MEASURED RATHER THAN ASSUMED. platform-config has
prune: true, so it deletes both profiles once, CDI recreates them with empty spec,
and the new tier re-applies the overrides ~30-60s later. Compared our override
against CDI's unaided inference for the same Longhorn provisioner on dev:
  longhorn-vm (we override)     spec RWX/Block  -> status ReadWriteMany/Block
  longhorn-static (no override) spec unset      -> status ReadWriteOnce/Block
Both infer cloneStrategy: snapshot. So cloneStrategy is NOT at risk; accessModes
IS — unaided CDI gives RWO. A DataVolume provisioned on longhorn-vm inside the
window would be stamped RWO/Block and be PERMANENTLY non-live-migratable. Flux can
no longer cause it (apps-vms gates on the new tier); a human must not do it by hand.
Corroborating evidence that the recreate happens at all: dev has 5 StorageClasses
and 5 StorageProfiles, three with fluxOwner=NONE, spec unset and status populated
— CDI creating and inferring them with no Flux involvement.

MERGE PRECONDITION: `flux get kustomization platform-config` must be Ready on the
target first. If it is not, the profiles are pruned and sit at CDI defaults until
it recovers — and prod was in that state hours earlier. Fallback is the two-step
the Cilium move used (merge with prune: false, verify the ownership label moved,
restore prune: true).

substituteFrom: cluster-vars is declared even though the manifest has no ${TOKEN},
deliberately: conformance/tests/l0-static/flux-postbuild-substitution only audits
paths whose Kustomization declares it, so omitting it would move the file OUT of
the audited set — a blind spot for a future literal-token ship. Gate confirms it
stayed in (path=./platform-config-cdi files=2 defined=0 hazards=0). No SOPS
decryption stanza: the moved file is two plain CRs, so no overlay change was needed.

VERIFIED INDEPENDENTLY OF THE AGENT: platform-config renders 0 StorageProfile
while keeping the CDI and KubeVirt CRs; platform-config-cdi renders exactly the
two profiles; the graph is byte-identical across dev and prod with apps-vms
carrying both edges and no cycle. Full CI gate PASS.

KNOWN FOLLOW-UP: bootstrap/standup.sh TIER_ORDER does not yet include
platform-config-cdi, so `resume` will not wait on it. Another agent holds that
file; the PM will add it.

Refs R-GITOPS-01, R-ENV-02.

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

2026-09-06 22:14:19 -05:00

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clusters/

Flux entrypoints and the environment-overlay model (R-ENV-02, R-GITOPS-01/02/03).

Governing spec: docs/05-gitops-and-delivery.md, docs/02-environments-and-provisioning.md, ADR-0004 (Flux).

Phase 0 scaffolding only. These are structurally-correct stubs. No cluster exists — nothing here reconciles until WS-INFRA delivers a cluster and bootstraps Flux (roadmap Phase 1).

Layout — base + overlay (never fork the base)

clusters/
  base/                 shared Flux objects (one authoring, both environments)
    flux-system.yaml    GitRepository — the reconciliation source (bootstrap → Gitea)
    platform.yaml       Flux Kustomization → ./platform   (reconciles first)
    apps-wave-0.yaml    Flux Kustomization → ./apps/wave-0 (dependsOn platform-config)
    apps-wave-1.yaml    Flux Kustomization → ./apps/wave-1 (dependsOn apps-wave-0)
    apps-wave-2.yaml    Flux Kustomization → ./apps/wave-N (dependsOn apps-wave-N-1)
    cluster-vars.yaml   ConfigMap of overlay knobs (BASE defaults)
    kustomization.yaml
  dev/                  ACTIVE build target — patches cluster-vars with dev values only
    kustomization.yaml
  prod/                 DESIGN-ONLY until roadmap Phase 7 — patches cluster-vars with prod values only
    kustomization.yaml

How the overlay model satisfies R-ENV-02

The base authors the reconciliation graph once. platform.yaml and the app-wave Kustomizations (apps-wave-0/1/2.yaml — the single apps.yaml was retired; apps-vms.yaml deliberately omits it, see below) declare postBuild.substituteFrom the cluster-vars ConfigMap. Platform and app manifests use ${TOKEN} placeholders for every value that legitimately differs between environments (issuer, replica counts, storage sizes, retention, node placement).

clusters/dev and clusters/prod differ ONLY by the values they patch into cluster-vars — they add no resources of their own and never copy/fork a base manifest. Promotion to prod (docs/02) is a change to the prod overlay's variables, nothing else.

LAN addressing is a knob, not a literal (fixed 2026-08-31)

Until 2026-08-31 the base manifests hardcoded the dev LAN: the k3s API host Cilium dials, the Cilium LB IP pool range, the pinned crafty/unifi L4 VIPs and the off-cluster S3 backup endpoint. That broke R-ENV-02 outright — clusters/prod would have rendered dev addresses (192.168.1.x) onto the prod LAN (192.168.2.x). They are now the cluster-vars "LAN addressing" block (K3S_API_HOST, CILIUM_LB_POOL_START/_STOP, UNIFI_L4_VIP, CRAFTY_L4_VIP, S3_BACKUP_ENDPOINT, alongside the pre-existing GATEWAY_VIP), set explicitly by BOTH overlays.

Two rules when touching that block:

Substitution coverage. A ${TOKEN} only resolves in a path whose Flux Kustomization declares postBuild.substituteFrom: cluster-vars; anywhere else the literal string ${TOKEN} ships to the cluster. apps-vms was the one path without it and now has it — which means every shell ${...} in a VM manifest's cloud-init must be escaped $${...} (see clusters/base/apps-vms.yaml for the full envsubst escape contract).
GATEWAY_VIP must be inside CILIUM_LB_POOL_START..STOP, and in practice equal to START: the shared Gateway pins no address, so Cilium LB-IPAM gives it the pool's first free IP while split-horizon CoreDNS answers with ${GATEWAY_VIP}. A VIP outside the pool blackholes in-cluster hairpin traffic while the Gateway still looks healthy.

Values the operator has not decided are TBD-PROD-* placeholders, not guesses: prod inherits the DEV base defaults if an overlay op is simply omitted, so an invalid value that fails loudly is strictly safer than a plausible one that quietly comes up on the wrong network.

How Flux is pointed at an environment

flux bootstrap (run by WS-INFRA in Phase 1) targets one environment's path per cluster:

# dev cluster
flux bootstrap ... --path=clusters/dev
# prod cluster (Phase 7 only — design-only until then)
flux bootstrap ... --path=clusters/prod

Bootstrap materializes the flux-system Kustomization that renders the chosen overlay, which pulls in base/ and applies the env-scoped cluster-vars.

Reconciliation order

GitRepository (flux-system)
        │
        ▼
Kustomization: platform  (./platform, substituteFrom cluster-vars)
        │  healthy
        ▼
Kustomization: apps-wave-0  (./apps/wave-0, dependsOn platform-config, substituteFrom cluster-vars)
        │  healthy
        ▼
Kustomization: apps-wave-1  (./apps/wave-1, dependsOn apps-wave-0)
        │  healthy
        ▼
Kustomization: apps-wave-N  (./apps/wave-N, dependsOn apps-wave-N-1)

Second-order CRDs need a THIRD pass (`platform-config-cdi`, added 2026-09-05)

The controllers/configs split (platform → platform-config) assumes a CRD is registered by the controller install. CDI breaks that: cdi-operator.yaml registers only cdis.cdi.kubevirt.io, and cdi-operator creates storageprofiles / datavolumes / datasources only after it has reconciled the CDI CR. Since kustomize-controller server-side dry-runs every object in a pass before applying any of them, having the CDI CR and the CDI StorageProfiles in one pass was a deadlock, not a race: unknown kind → pass aborts → CR never applied → CRD never created → platform-config can never converge → every tier below it blocked. Invisible on dev (its CDI CRDs have existed for months); it cost 12h on prod's cold start.

So there is a third tier, platform-config-cdi (./platform-config-cdi, dependsOn: platform-config), and a rule:

A CR belongs in platform-config-cdi, not platform-config, when the CRD it needs is created by a controller at runtime rather than by a manifest in git.

apps-vms dependsOn it as well as platform-config, because CDI reads StorageProfile/longhorn-vm at DataVolume provisioning time — a VM disk provisioned before that profile exists is stamped RWO/Filesystem and is permanently not live-migratable.

Wave 0 dependsOn platform-config (transitively platform) so CNI/storage/TLS/DNS/gateway exist before any workload reconciles. The app tier is split into dependency-ordered WAVES (catalog/render.py --emit-waves): each apps-wave-<N> health-gates (wait:true) ONLY its own wave, so a crashloop in a later wave can no longer stall an earlier wave or block new revisions. See DESIGN-waves.md for the wave table + cutover runbook.

TODOs (later phases — do not action in Phase 0)

Source cutover (WS-GITOPS, Phase 6): base/flux-system.yaml currently points at the bootstrap source. After Gitea is onboarded, repoint spec.url to gitea.home.keithjackson.dev and keep an off-cluster mirror (spec docs/05 "Source-of-truth", CONTRIBUTING.md).
SOPS decryption (WS-SEC, Phase 1): add spec.decryption.provider: sops (age secret name only, never plaintext) to the platform/apps Kustomizations once the age key is bootstrapped (ADR-0007).
Split ordered Flux Kustomizations if intra-platform ordering needs to be explicit (e.g. a separate cilium/longhorn Kustomization others dependsOn).

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