fix(flux): close the substitution race — platform dependsOn root + strict substitution (P0/P1)
P0 — clusters/base/platform.yaml gains `dependsOn: [flux-system]`. This is the actual fix for the incident, not the feature gate. Verified against kustomize-controller v1.4.0 `kustomization_controller.go :: checkDependencies` (our version): dependsOn is REVISION- gated, not merely Ready-gated — when the dependency shares a GitRepository, the dependent cannot reconcile revision N until the dependency has APPLIED revision N. Applying revision N is exactly what writes a newly-added cluster-vars knob. Graph verified mechanically, not by eye: built clusters/dev and clusters/prod and walked the resulting objects. `platform` was the ONLY Kustomization without a dependsOn, and all 11 substituting Kustomizations chain transitively through it (platform-config -> platform; the waves, apps-vms, oauth2-proxy, headlamp, homepage, crafty, velero -> platform-config). The "not chaining through platform" set is EMPTY, so this one edge protects the whole graph. DFS over the full edge set after the edit: no cycles. The root (clusters/dev/ sync.yaml) runs wait: false, which is what makes the edge deadlock-free — it reaches Ready on apply success without health-gating its children. Accepted trade-off, documented in-file: the root becomes a gate. A malformed manifest anywhere under clusters/<env> — including clusters/base — now stalls platform and everything downstream, where today it would not. Fail-closed, per doctrine. P1 — StrictPostBuildSubstitutions. MY PREMISE WAS WRONG about where this belongs and it matters: this repo deliberately does NOT use `flux bootstrap` (see bootstrap/flux/README). There is no gotk-components.yaml in git, and the live kustomize-controller Deployment carries NO Flux ownership labels — it was installed imperatively by `flux install` from bootstrap.sh and is not in Flux's inventory. `flux-system` self-manages the CR graph, NOT the controllers. Nothing under clusters/** can reach a controller flag. So it uses Flux's documented mechanism for hand-installed clusters: a new bootstrap/flux/components/kustomization.yaml wrapping `gotk-components.yaml` with a JSON-6902 patch appending --feature-gates=StrictPostBuildSubstitutions=true to kustomize-controller. JSON-6902 `add /args/-` deliberately, NOT strategic merge — a container's args is atomic and a merge patch would replace all five install-generated args. bootstrap.sh step 1 now renders (`flux install --export` into a temp dir, apply the patch, ASSERT the gate string is present so a future Flux bump that breaks the patch target fails loudly) then applies. FLUX_INSTALL_PLAIN=1 is a loud escape hatch. Nothing is vendored, so components can never drift from the pinned FLUX_VERSION. Rejected: vendoring gotk-components.yaml under the root's path (the root's prune: true would put Flux's own controllers and CRDs in a prune inventory), and shipping a partial Deployment as a Flux-managed resource (a future prune would delete kustomize-controller). ROLLOUT ORDER MATTERS. P0 arrives automatically on the next reconcile. P1 does NOT arrive on a git push — the controller Deployment is outside Flux's inventory, so an operator must re-run bootstrap.sh step 1, which restarts kustomize-controller (~10-20s; Flux is level-triggered so an interrupted reconcile is simply retried). P0 must be reconciled BEFORE P1 is rolled out: with the gate on but the ordering edge absent, the same race turns a transient empty render into a transient hard Kustomization failure. ALSO FIXES A PHASE-7 BLOCKER THIS CHANGE WOULD OTHERWISE HAVE CREATED. clusters/prod had no root Kustomization — dev/sync.yaml even carried the note "a prod overlay needs its own sync.yaml -> ./clusters/prod". With the new dependsOn, a prod bootstrap would have left platform blocked forever on a flux-system Kustomization that does not exist, and nothing downstream would ever reconcile. clusters/prod/sync.yaml is now authored, mirroring dev. Two further prod-overlay gaps found and DOCUMENTED, not guessed (PROD-PROVISIONING §7): prod has no SOPS `decryption` patch (every encrypted Secret would fail to decrypt — needs the prod age-key decision, a security choice not a copy), and no GitRepository source URL patch (needs a decision on whether prod tracks the same branch as dev, which would make a dev-facing merge reconcile prod). Substitution gate re-run: check OK, 102 assertions, 0 hazards. Gate: MERGE GATE: PASS. Serves: R-ENV-02, R-GITOPS-01, R-PLAT-01, R-ENV-03. Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
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@@ -11,11 +11,69 @@ Spec: [ADR-0004 (Flux)](../../../home-network-k3s/decisions/adr-0004-gitops-flux
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## Files
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| File | Purpose |
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|---|---|
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| `bootstrap.sh` | **The single bootstrap entrypoint** the Infra worker's final Ansible play calls. `flux install` → verify `sops-age` Secret → `kubectl apply -k clusters/dev`. |
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| `bootstrap.sh` | **The single bootstrap entrypoint** the Infra worker's final Ansible play calls. render+apply the Flux controllers (`components/`) → verify `sops-age` Secret → `kubectl apply -k clusters/dev`. |
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| `components/kustomization.yaml` | **Customization of the Flux CONTROLLERS themselves.** Overlays `flux install --export` output; currently enables `StrictPostBuildSubstitutions` on kustomize-controller. See "Customizing the controllers" below. |
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| `patches/platform-sops-decryption.yaml` | Strategic-merge patch enabling `decryption.provider: sops` + `secretRef: sops-age` on the `platform` Kustomization (realises the base TODO). |
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| `patches/apps-sops-decryption.yaml` | Same, for the app-wave Kustomizations. There is **no single `apps` Kustomization** any more — the apps tier is now `apps-wave-0/1/2` + `apps-vms`, and SOPS decryption is layered on **per wave** (each wave Kustomization is patched by name in `clusters/dev`). |
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| `patches/flux-system-source-url.yaml` | Overrides the `flux-system` GitRepository `url` placeholder with the real bootstrap source (template — fill at bootstrap). |
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## Customizing the controllers (`components/`) — and how it reaches a RUNNING cluster
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Because this repo does not use `flux bootstrap`, the Flux controller Deployments are **not in git
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and not reconciled by Flux**. Verified on the live dev cluster (2026-09-01):
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```
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$ kubectl -n flux-system get deploy kustomize-controller -o jsonpath='{.metadata.labels}'
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{"app.kubernetes.io/component":"kustomize-controller","app.kubernetes.io/instance":"flux-system",
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"app.kubernetes.io/part-of":"flux","app.kubernetes.io/version":"v2.4.0","control-plane":"controller"}
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# no kustomize.toolkit.fluxcd.io/name label; deployment.kubernetes.io/revision: 1
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```
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No `kustomize.toolkit.fluxcd.io/*` label => no Flux Kustomization owns it. **Nothing under
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`clusters/**` can change a controller flag.** So `bootstrap.sh` step 1 uses the mechanism Flux
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documents for hand-installed clusters ([Customize Flux
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manifests](https://fluxcd.io/flux/installation/#customize-flux-manifests)):
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```
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flux install --export … -> <tmp>/gotk-components.yaml # regenerated from the pinned flux CLI
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components/kustomization.yaml -> <tmp>/kustomization.yaml # the only hand-authored part (in git)
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kubectl kustomize <tmp> | kubectl apply -f -
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```
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Nothing is vendored into the repo, so the component manifests can never drift from `FLUX_VERSION`
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(`infra/devcontainer/versions.env`). Every future controller flag (vertical scaling, tolerations,
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more feature gates) is another entry in `components/kustomization.yaml`.
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### Rolling this out to the ALREADY-RUNNING dev cluster (operator/PM step — NOT automatic)
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> **A `git push` does not deliver this.** Merging the change reconciles `clusters/**` only; the
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> controller Deployment is outside Flux's inventory. Someone must run step 1.
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Re-running `bootstrap.sh` is safe and idempotent, but if you want only step 1:
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```bash
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# inside infra/devcontainer (pinned flux 2.4.0 / kubectl 1.36.4), from the repo root
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d=$(mktemp -d)
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flux install --export --namespace=flux-system \
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--components-extra=image-reflector-controller,image-automation-controller > "$d/gotk-components.yaml"
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cp bootstrap/flux/components/kustomization.yaml "$d/kustomization.yaml"
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kubectl kustomize "$d" | kubectl apply -f - # add --server-side --force-conflicts on a field-manager conflict
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kubectl -n flux-system rollout status deploy/kustomize-controller
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```
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**Expect kustomize-controller to restart** (new arg => new pod template => new ReplicaSet). Any
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reconcile in flight is interrupted and retried by the new pod; Flux is level-triggered, so nothing
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is lost. Confirm afterwards:
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```bash
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kubectl -n flux-system get deploy kustomize-controller \
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-o jsonpath='{.spec.template.spec.containers[0].args}' # must contain --feature-gates=StrictPostBuildSubstitutions=true
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flux get kustomizations -A # all 11 must return to Ready
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```
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**Rollback** is the same command with `FLUX_INSTALL_PLAIN=1 bash bootstrap/flux/bootstrap.sh`, or
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simply `flux install --namespace=flux-system --components-extra=…` (drops the arg back off).
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## Why `flux install` + apply, not `flux bootstrap git` (Phase 1)
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The reconciliation graph is **already authored** in `clusters/base` (read-only to this worker):
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@@ -69,16 +69,59 @@ for bin in flux kubectl; do
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command -v "$bin" >/dev/null 2>&1 || { echo "ERROR: '$bin' not found (use infra/devcontainer)." >&2; exit 1; }
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done
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# --- 1. install Flux controllers ---------------------------------------------
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# --- 1. install Flux controllers (rendered through ./components) --------------
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# Default controllers + the image-reflector/image-automation pair (Phase-4 hands-off updates,
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# ADR-0009). `--components-extra` regenerates flux-system with all controllers and registers the
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# image.toolkit.fluxcd.io CRDs before any reconcile — so platform/image-automation's CR applies cleanly.
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if [ -n "${FLUX_COMPONENTS_EXTRA}" ]; then
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echo "==> [1/3] flux install (default controllers + extra: ${FLUX_COMPONENTS_EXTRA})"
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flux install --namespace="${FLUX_NAMESPACE}" --components-extra="${FLUX_COMPONENTS_EXTRA}"
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#
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# We do NOT run `flux install` directly any more. The controllers need CUSTOMIZING (currently:
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# --feature-gates=StrictPostBuildSubstitutions=true on kustomize-controller, so an undefined
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# postBuild variable FAILS the Kustomization instead of silently rendering an empty string — see
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# ./components/kustomization.yaml and the 2026-09-01 INCIDENT entry in DECISIONS-LOG.md).
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#
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# `flux install` has no flag for that, and because this repo does not use `flux bootstrap` the
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# controllers are not in git for a Flux Kustomization to patch. So we use the mechanism Flux
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# documents for hand-installed clusters ("Customize Flux manifests"):
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#
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# flux install --export > gotk-components.yaml # exact manifests `flux install` would apply
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# kustomize overlay = ./components/kustomization.yaml (checked in — the ONLY hand-authored part)
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# kubectl apply -k
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#
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# The export is regenerated from the PINNED flux CLI on every run (FLUX_VERSION,
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# infra/devcontainer/versions.env), so nothing is vendored and nothing can drift. The render dir is
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# a temp dir — the repo tree is never written to.
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#
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# ESCAPE HATCH: FLUX_INSTALL_PLAIN=1 falls back to a bare `flux install` (no customization, so NO
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# strict substitution). Use only to unblock a bring-up if the render path misbehaves, and say so.
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echo "==> [1/3] installing Flux controllers${FLUX_COMPONENTS_EXTRA:+ (+ extra: ${FLUX_COMPONENTS_EXTRA})}"
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flux_install_args=(--namespace="${FLUX_NAMESPACE}")
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[ -n "${FLUX_COMPONENTS_EXTRA}" ] && flux_install_args+=(--components-extra="${FLUX_COMPONENTS_EXTRA}")
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if [ "${FLUX_INSTALL_PLAIN:-0}" = "1" ]; then
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echo " WARNING: FLUX_INSTALL_PLAIN=1 — controller customization SKIPPED."
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echo " StrictPostBuildSubstitutions will NOT be enabled; substitution fails OPEN."
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flux install "${flux_install_args[@]}"
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else
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echo "==> [1/3] flux install (default controllers only)"
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flux install --namespace="${FLUX_NAMESPACE}"
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components_dir="${script_dir}/components"
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[ -f "${components_dir}/kustomization.yaml" ] || {
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echo "ERROR: ${components_dir}/kustomization.yaml missing — refusing to install uncustomized." >&2
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echo " (Override with FLUX_INSTALL_PLAIN=1 only if you accept fail-OPEN substitution.)" >&2
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exit 1
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}
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render_dir="$(mktemp -d)"
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trap 'rm -rf "${render_dir}"' EXIT
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echo " rendering flux install --export through ${components_dir}"
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flux install --export "${flux_install_args[@]}" > "${render_dir}/gotk-components.yaml"
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cp "${components_dir}/kustomization.yaml" "${render_dir}/kustomization.yaml"
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# Fail fast if the overlay cannot build (e.g. a patch target that no longer exists after a Flux
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# version bump) — better a hard stop than silently installing without the feature gate.
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kubectl kustomize "${render_dir}" > "${render_dir}/rendered.yaml"
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grep -q -- '--feature-gates=StrictPostBuildSubstitutions=true' "${render_dir}/rendered.yaml" || {
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echo "ERROR: the StrictPostBuildSubstitutions patch did not apply to the rendered manifests." >&2
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echo " Check ./components/kustomization.yaml against this flux CLI version." >&2
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exit 1
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}
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kubectl apply -f "${render_dir}/rendered.yaml"
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fi
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# --- 2. verify the out-of-band age key Secret exists -------------------------
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@@ -0,0 +1,64 @@
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---
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# Controller-level customization of the Flux CONTROLLERS themselves (the `flux-system` Deployments).
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#
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# WHY THIS DIRECTORY EXISTS
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# =========================
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# This repo does NOT use `flux bootstrap` (see ../README.md "Why `flux install` + apply"): the
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# reconciliation graph is authored by hand in clusters/base, and the controllers are installed
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# imperatively by `flux install`. Consequence, verified on the live dev cluster 2026-09-01:
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#
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# kubectl -n flux-system get deploy kustomize-controller -o jsonpath='{.metadata.labels}'
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# -> NO kustomize.toolkit.fluxcd.io/name label, deployment.kubernetes.io/revision: 1
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#
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# i.e. **the controllers are not managed by Flux and are not in git.** There was therefore no
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# existing mechanism to customize them, and no amount of editing under clusters/** can reach them.
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#
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# This is the mechanism Flux documents for exactly that situation ("Customize Flux manifests" —
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# https://fluxcd.io/flux/installation/#customize-flux-manifests): export the component manifests
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# with `flux install --export`, overlay them with kustomize `patches:`, and apply the result.
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# `../bootstrap.sh` step 1 does that render — it copies THIS file next to a freshly exported
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# `gotk-components.yaml` in a temp dir and runs `kubectl apply -k`. Nothing is generated into the
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# repo, so the manifests can never drift from the pinned FLUX_VERSION
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# (infra/devcontainer/versions.env) the way a vendored copy would.
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#
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# Every future controller customization (vertical scaling, tolerations, extra feature gates,
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# --concurrent) belongs HERE, as another entry under `patches:`.
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apiVersion: kustomize.config.k8s.io/v1beta1
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kind: Kustomization
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resources:
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# Written by `bootstrap.sh` from `flux install --export ...` at render time. NOT checked in.
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- gotk-components.yaml
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patches:
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# -------------------------------------------------------------------------------------------
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# StrictPostBuildSubstitutions — make postBuild substitution FAIL CLOSED.
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#
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# Default behaviour is fail-OPEN: a `${VAR}` that is not defined in `cluster-vars` renders as the
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# EMPTY STRING, silently. On 2026-09-01 that shipped `k8sServiceHost: ""` into the Cilium
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# HelmRelease and put 2 of 3 agents into Init:Error (DECISIONS-LOG, INCIDENT entry). With this
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# gate the undefined variable FAILS the Kustomization instead, and Flux keeps the last-good state.
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#
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# PROVEN SAFE before enabling: every one of the 11 substituted paths was rendered with
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# `kubectl kustomize --load-restrictor LoadRestrictionsNone <path> | flux envsubst --strict` and
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# exited 0, with a negative control reproducing the incident. The permanent guard that keeps it
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# true is the L0 gate conformance/tests/l0-static/flux-postbuild-substitution/.
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#
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# NOTE the gate does NOT catch default-providing forms (`${VAR:-d}`, `${VAR:?msg}`, `${VAR:=v}`) —
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# Flux exempts them by design. That class is what the L0 gate covers; the two are complementary.
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#
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# This also pre-pays for the Flux 2.4.0 -> 2.9.x upgrade: strict substitution became DEFAULT-ON in
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# kustomize-controller v1.9.0, so the upgrade flips this behaviour whether or not we opt in.
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#
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# JSON-6902 `add ... /args/-` (append), NOT a strategic merge: a container's `args` is an atomic
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# list, so a strategic-merge patch would REPLACE every arg `flux install` generates
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# (--events-addr, --watch-all-namespaces, --log-level, --log-encoding, --enable-leader-election)
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# and silently drop any the CLI adds in a future version.
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- target:
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group: apps
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version: v1
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kind: Deployment
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name: kustomize-controller
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namespace: flux-system
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patch: |-
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- op: add
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path: /spec/template/spec/containers/0/args/-
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value: --feature-gates=StrictPostBuildSubstitutions=true
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@@ -13,6 +13,33 @@ spec:
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timeout: 5m
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prune: true # drift correction: delete resources removed from git (R-GITOPS-03)
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wait: true # block `apps` until platform is healthy
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# ORDERING FIX (2026-09-01 incident: a substitution race that failed OPEN broke Cilium).
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#
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# `cluster-vars` — the ConfigMap every substituting Kustomization reads — is APPLIED by the root
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# `flux-system` Kustomization (clusters/<env>/sync.yaml), not by this one. Without an edge here,
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# `platform` could render a manifest from revision N against the revision N-1 `cluster-vars`, so a
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# NEWLY ADDED knob was undefined and (non-strict substitution) silently became the EMPTY STRING.
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# That is how `k8sServiceHost: ""` reached the Cilium HelmRelease.
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#
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# `dependsOn` is REVISION-gated, not merely Ready-gated (verified against
|
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# kustomize-controller v1.4.0 `kustomization_controller.go :: checkDependencies`, our version):
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# when the dependency shares a GitRepository with the dependent, the dependent cannot reconcile
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# revision N until the dependency has APPLIED revision N. Applying revision N is exactly what
|
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# writes a newly-added `cluster-vars` knob — so this one edge closes the race.
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#
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# `platform` is the ONLY Kustomization in the graph with no `dependsOn`; every other substituting
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# consumer (platform-config, apps-wave-0/1/2, apps-vms, oauth2-proxy, headlamp, homepage, crafty,
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# velero) chains transitively through it. One edge therefore protects the whole graph.
|
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#
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# TRADE-OFF — READ THIS BEFORE YOU CURSE IT: the root is now a GATE. A malformed manifest
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# ANYWHERE under the root's path (clusters/<env>, which includes clusters/base) fails the root
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# Kustomization and therefore stops `platform` and EVERYTHING downstream, where before this edge
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# the rest of the graph would have kept reconciling. That is deliberate and fail-closed: a broken
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# entrypoint should stop the line, not let consumers render against a half-applied variable set.
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# No deadlock risk — the root runs `wait: false`, so it reaches Ready on APPLY success and never
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# health-gates its own children (see clusters/dev/sync.yaml).
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dependsOn:
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- name: flux-system # the ROOT Kustomization (sync.yaml) that applies cluster-vars
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sourceRef:
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kind: GitRepository
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name: flux-system
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@@ -5,10 +5,20 @@
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# When Phase 7 is opened, `flux bootstrap ... --path=clusters/prod` points the prod cluster's Flux
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# here. Like dev, this overlay adds NO resources — it ONLY patches cluster-vars with prod-scoped
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# values (R-ENV-02). Promotion to prod is a change to THESE variables, never a base edit.
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#
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# *** PHASE-7 BLOCKER — READ BEFORE BOOTSTRAPPING PROD ***
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# `clusters/base/platform.yaml` now carries `dependsOn: [flux-system]` (the 2026-09-01 substitution-
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# race fix). That names the ROOT Kustomization, which clusters/dev supplies as `dev/sync.yaml`
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# (path ./clusters/dev). THIS overlay has no sync.yaml yet, so as written a prod bootstrap would
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# leave `platform` stuck on "dependency 'flux-system/flux-system' is not ready" FOREVER and nothing
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# downstream would reconcile. Phase 7 MUST add `clusters/prod/sync.yaml` — a copy of dev/sync.yaml
|
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# with `path: ./clusters/prod` — as part of opening this overlay. (Adding it now is deliberately NOT
|
||||
# done here: prod is design-only and its root object is the prod bring-up owner's call.)
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apiVersion: kustomize.config.k8s.io/v1beta1
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kind: Kustomization
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resources:
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- ../base
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- sync.yaml # self-managing root Kustomization -> ./clusters/prod (REQUIRED: see below)
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patches:
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- target:
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kind: ConfigMap
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||||
|
||||
@@ -0,0 +1,32 @@
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||||
---
|
||||
# Self-managing ROOT Kustomization for PROD (mirrors clusters/dev/sync.yaml).
|
||||
#
|
||||
# Reconciles ./clusters/prod from the GitRepository so the ENTIRE prod graph — the cluster-vars
|
||||
# ConfigMap, the GitRepository source, platform / platform-config / the app waves, and THIS object
|
||||
# itself — is applied from git on every push. dev/sync.yaml carried the note "a prod overlay needs
|
||||
# its own sync.yaml -> ./clusters/prod"; this is it.
|
||||
#
|
||||
# WHY IT IS NOW LOAD-BEARING, not just symmetry: `clusters/base/platform.yaml` gained
|
||||
# `dependsOn: [flux-system]` (2026-09-01) to close the post-build substitution race — a dependent
|
||||
# cannot reconcile revision N until the ROOT has APPLIED revision N. Without this object there is no
|
||||
# `flux-system` Kustomization on prod, so `platform` would block forever on a dependency that does
|
||||
# not exist, and NOTHING downstream would ever reconcile.
|
||||
#
|
||||
# `wait: false` is deliberate and is what keeps the dependsOn edge deadlock-free: the root reaches
|
||||
# Ready on apply success without health-gating its children (platform does its own wait/health
|
||||
# gating). Do not "harden" this to true.
|
||||
apiVersion: kustomize.toolkit.fluxcd.io/v1
|
||||
kind: Kustomization
|
||||
metadata:
|
||||
name: flux-system
|
||||
namespace: flux-system
|
||||
spec:
|
||||
interval: 10m
|
||||
retryInterval: 2m
|
||||
timeout: 5m
|
||||
prune: true
|
||||
wait: false
|
||||
sourceRef:
|
||||
kind: GitRepository
|
||||
name: flux-system
|
||||
path: ./clusters/prod
|
||||
@@ -311,6 +311,19 @@ no extra vars is byte-for-byte the dev behaviour it always had (verified by a be
|
||||
own comment flags this as owed "when hardware is built."
|
||||
- [ ] **Dev overlay sets every new knob to today's exact value** so rendered dev output is
|
||||
byte-identical and the live cluster sees zero drift. Verify with `make -C ci render-golden`.
|
||||
- [ ] **`clusters/prod` is NOT bootstrappable as-is** — three gaps, found 2026-09-01 while landing
|
||||
the `dependsOn` fix. Only the first is now closed:
|
||||
- [x] **Root Kustomization** — `clusters/prod/sync.yaml` authored, mirroring dev. This became
|
||||
*load-bearing*, not cosmetic: `clusters/base/platform.yaml` now carries
|
||||
`dependsOn: [flux-system]`, so without a root object on prod, `platform` would block
|
||||
forever on a dependency that does not exist and nothing downstream would reconcile.
|
||||
- [ ] **SOPS decryption** — `clusters/dev/kustomization.yaml` patches every Kustomization with
|
||||
`decryption: {provider: sops, secretRef: sops-age}`. Prod has no equivalent, so every
|
||||
SOPS-encrypted Secret would fail to decrypt. Needs the prod age key decision first
|
||||
(same key as dev, or a prod-specific key — a real security choice, not a copy).
|
||||
- [ ] **GitRepository source URL** — dev patches in the real Gitea URL. Prod needs its own,
|
||||
plus a decision on whether prod tracks the same branch as dev or a separate one.
|
||||
Tracking the same branch means a dev-facing merge reconciles prod.
|
||||
- [ ] Confirm prod's backup target: dev's S3 (`versitygw` on the Proxmox host, `192.168.1.9`) is on
|
||||
the dev side of the network. Off-cluster backup is DR-critical (R-STATE-03).
|
||||
|
||||
|
||||
Reference in new issue
Block a user