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]>

bootstrap/flux/README.md

@@ -11,11 +11,69 @@ Spec: [ADR-0004 (Flux)](../../../home-network-k3s/decisions/adr-0004-gitops-flux
 ## Files
 | File | Purpose |
 |---|---|
-| `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`. |
+| `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`. |
+| `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. |
 | `patches/platform-sops-decryption.yaml` | Strategic-merge patch enabling `decryption.provider: sops` + `secretRef: sops-age` on the `platform` Kustomization (realises the base TODO). |
 | `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`). |
 | `patches/flux-system-source-url.yaml` | Overrides the `flux-system` GitRepository `url` placeholder with the real bootstrap source (template — fill at bootstrap). |
 
+## Customizing the controllers (`components/`) — and how it reaches a RUNNING cluster
+
+Because this repo does not use `flux bootstrap`, the Flux controller Deployments are **not in git
+and not reconciled by Flux**. Verified on the live dev cluster (2026-09-01):
+
+```
+$ kubectl -n flux-system get deploy kustomize-controller -o jsonpath='{.metadata.labels}'
+{"app.kubernetes.io/component":"kustomize-controller","app.kubernetes.io/instance":"flux-system",
+ "app.kubernetes.io/part-of":"flux","app.kubernetes.io/version":"v2.4.0","control-plane":"controller"}
+# no kustomize.toolkit.fluxcd.io/name label; deployment.kubernetes.io/revision: 1
+```
+
+No `kustomize.toolkit.fluxcd.io/*` label => no Flux Kustomization owns it. **Nothing under
+`clusters/**` can change a controller flag.** So `bootstrap.sh` step 1 uses the mechanism Flux
+documents for hand-installed clusters ([Customize Flux
+manifests](https://fluxcd.io/flux/installation/#customize-flux-manifests)):
+
+```
+flux install --export …  ->  <tmp>/gotk-components.yaml     # regenerated from the pinned flux CLI
+components/kustomization.yaml -> <tmp>/kustomization.yaml   # the only hand-authored part (in git)
+kubectl kustomize <tmp> | kubectl apply -f -
+```
+
+Nothing is vendored into the repo, so the component manifests can never drift from `FLUX_VERSION`
+(`infra/devcontainer/versions.env`). Every future controller flag (vertical scaling, tolerations,
+more feature gates) is another entry in `components/kustomization.yaml`.
+
+### Rolling this out to the ALREADY-RUNNING dev cluster (operator/PM step — NOT automatic)
+
+> **A `git push` does not deliver this.** Merging the change reconciles `clusters/**` only; the
+> controller Deployment is outside Flux's inventory. Someone must run step 1.
+
+Re-running `bootstrap.sh` is safe and idempotent, but if you want only step 1:
+
+```bash
+# inside infra/devcontainer (pinned flux 2.4.0 / kubectl 1.36.4), from the repo root
+d=$(mktemp -d)
+flux install --export --namespace=flux-system \
+  --components-extra=image-reflector-controller,image-automation-controller > "$d/gotk-components.yaml"
+cp bootstrap/flux/components/kustomization.yaml "$d/kustomization.yaml"
+kubectl kustomize "$d" | kubectl apply -f -      # add --server-side --force-conflicts on a field-manager conflict
+kubectl -n flux-system rollout status deploy/kustomize-controller
+```
+
+**Expect kustomize-controller to restart** (new arg => new pod template => new ReplicaSet). Any
+reconcile in flight is interrupted and retried by the new pod; Flux is level-triggered, so nothing
+is lost. Confirm afterwards:
+
+```bash
+kubectl -n flux-system get deploy kustomize-controller \
+  -o jsonpath='{.spec.template.spec.containers[0].args}'   # must contain --feature-gates=StrictPostBuildSubstitutions=true
+flux get kustomizations -A                                  # all 11 must return to Ready
+```
+
+**Rollback** is the same command with `FLUX_INSTALL_PLAIN=1 bash bootstrap/flux/bootstrap.sh`, or
+simply `flux install --namespace=flux-system --components-extra=…` (drops the arg back off).
+
 ## Why `flux install` + apply, not `flux bootstrap git` (Phase 1)
 
 The reconciliation graph is **already authored** in `clusters/base` (read-only to this worker):

bootstrap/flux/bootstrap.sh

@@ -69,16 +69,59 @@ for bin in flux kubectl; do
   command -v "$bin" >/dev/null 2>&1 || { echo "ERROR: '$bin' not found (use infra/devcontainer)." >&2; exit 1; }
 done
 
-# --- 1. install Flux controllers ---------------------------------------------
+# --- 1. install Flux controllers (rendered through ./components) --------------
 # Default controllers + the image-reflector/image-automation pair (Phase-4 hands-off updates,
 # ADR-0009). `--components-extra` regenerates flux-system with all controllers and registers the
 # image.toolkit.fluxcd.io CRDs before any reconcile — so platform/image-automation's CR applies cleanly.
-if [ -n "${FLUX_COMPONENTS_EXTRA}" ]; then
-  echo "==> [1/3] flux install (default controllers + extra: ${FLUX_COMPONENTS_EXTRA})"
-  flux install --namespace="${FLUX_NAMESPACE}" --components-extra="${FLUX_COMPONENTS_EXTRA}"
+#
+# We do NOT run `flux install` directly any more. The controllers need CUSTOMIZING (currently:
+# --feature-gates=StrictPostBuildSubstitutions=true on kustomize-controller, so an undefined
+# postBuild variable FAILS the Kustomization instead of silently rendering an empty string — see
+# ./components/kustomization.yaml and the 2026-09-01 INCIDENT entry in DECISIONS-LOG.md).
+#
+# `flux install` has no flag for that, and because this repo does not use `flux bootstrap` the
+# controllers are not in git for a Flux Kustomization to patch. So we use the mechanism Flux
+# documents for hand-installed clusters ("Customize Flux manifests"):
+#
+#     flux install --export  >  gotk-components.yaml     # exact manifests `flux install` would apply
+#     kustomize overlay      =  ./components/kustomization.yaml (checked in — the ONLY hand-authored part)
+#     kubectl apply -k
+#
+# The export is regenerated from the PINNED flux CLI on every run (FLUX_VERSION,
+# infra/devcontainer/versions.env), so nothing is vendored and nothing can drift. The render dir is
+# a temp dir — the repo tree is never written to.
+#
+# ESCAPE HATCH: FLUX_INSTALL_PLAIN=1 falls back to a bare `flux install` (no customization, so NO
+# strict substitution). Use only to unblock a bring-up if the render path misbehaves, and say so.
+echo "==> [1/3] installing Flux controllers${FLUX_COMPONENTS_EXTRA:+ (+ extra: ${FLUX_COMPONENTS_EXTRA})}"
+flux_install_args=(--namespace="${FLUX_NAMESPACE}")
+[ -n "${FLUX_COMPONENTS_EXTRA}" ] && flux_install_args+=(--components-extra="${FLUX_COMPONENTS_EXTRA}")
+
+if [ "${FLUX_INSTALL_PLAIN:-0}" = "1" ]; then
+  echo "    WARNING: FLUX_INSTALL_PLAIN=1 — controller customization SKIPPED."
+  echo "             StrictPostBuildSubstitutions will NOT be enabled; substitution fails OPEN."
+  flux install "${flux_install_args[@]}"
 else
-  echo "==> [1/3] flux install (default controllers only)"
-  flux install --namespace="${FLUX_NAMESPACE}"
+  components_dir="${script_dir}/components"
+  [ -f "${components_dir}/kustomization.yaml" ] || {
+    echo "ERROR: ${components_dir}/kustomization.yaml missing — refusing to install uncustomized." >&2
+    echo "       (Override with FLUX_INSTALL_PLAIN=1 only if you accept fail-OPEN substitution.)" >&2
+    exit 1
+  }
+  render_dir="$(mktemp -d)"
+  trap 'rm -rf "${render_dir}"' EXIT
+  echo "    rendering flux install --export through ${components_dir}"
+  flux install --export "${flux_install_args[@]}" > "${render_dir}/gotk-components.yaml"
+  cp "${components_dir}/kustomization.yaml" "${render_dir}/kustomization.yaml"
+  # Fail fast if the overlay cannot build (e.g. a patch target that no longer exists after a Flux
+  # version bump) — better a hard stop than silently installing without the feature gate.
+  kubectl kustomize "${render_dir}" > "${render_dir}/rendered.yaml"
+  grep -q -- '--feature-gates=StrictPostBuildSubstitutions=true' "${render_dir}/rendered.yaml" || {
+    echo "ERROR: the StrictPostBuildSubstitutions patch did not apply to the rendered manifests." >&2
+    echo "       Check ./components/kustomization.yaml against this flux CLI version." >&2
+    exit 1
+  }
+  kubectl apply -f "${render_dir}/rendered.yaml"
 fi
 
 # --- 2. verify the out-of-band age key Secret exists -------------------------

bootstrap/flux/components/kustomization.yaml

@@ -0,0 +1,64 @@
+---
+# Controller-level customization of the Flux CONTROLLERS themselves (the `flux-system` Deployments).
+#
+# WHY THIS DIRECTORY EXISTS
+# =========================
+# This repo does NOT use `flux bootstrap` (see ../README.md "Why `flux install` + apply"): the
+# reconciliation graph is authored by hand in clusters/base, and the controllers are installed
+# imperatively by `flux install`. Consequence, verified on the live dev cluster 2026-09-01:
+#
+#     kubectl -n flux-system get deploy kustomize-controller -o jsonpath='{.metadata.labels}'
+#     -> NO kustomize.toolkit.fluxcd.io/name label, deployment.kubernetes.io/revision: 1
+#
+# i.e. **the controllers are not managed by Flux and are not in git.** There was therefore no
+# existing mechanism to customize them, and no amount of editing under clusters/** can reach them.
+#
+# This is the mechanism Flux documents for exactly that situation ("Customize Flux manifests" —
+# https://fluxcd.io/flux/installation/#customize-flux-manifests): export the component manifests
+# with `flux install --export`, overlay them with kustomize `patches:`, and apply the result.
+# `../bootstrap.sh` step 1 does that render — it copies THIS file next to a freshly exported
+# `gotk-components.yaml` in a temp dir and runs `kubectl apply -k`. Nothing is generated into the
+# repo, so the manifests can never drift from the pinned FLUX_VERSION
+# (infra/devcontainer/versions.env) the way a vendored copy would.
+#
+# Every future controller customization (vertical scaling, tolerations, extra feature gates,
+# --concurrent) belongs HERE, as another entry under `patches:`.
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  # Written by `bootstrap.sh` from `flux install --export ...` at render time. NOT checked in.
+  - gotk-components.yaml
+patches:
+  # -------------------------------------------------------------------------------------------
+  # StrictPostBuildSubstitutions — make postBuild substitution FAIL CLOSED.
+  #
+  # Default behaviour is fail-OPEN: a `${VAR}` that is not defined in `cluster-vars` renders as the
+  # EMPTY STRING, silently. On 2026-09-01 that shipped `k8sServiceHost: ""` into the Cilium
+  # HelmRelease and put 2 of 3 agents into Init:Error (DECISIONS-LOG, INCIDENT entry). With this
+  # gate the undefined variable FAILS the Kustomization instead, and Flux keeps the last-good state.
+  #
+  # PROVEN SAFE before enabling: every one of the 11 substituted paths was rendered with
+  # `kubectl kustomize --load-restrictor LoadRestrictionsNone <path> | flux envsubst --strict` and
+  # exited 0, with a negative control reproducing the incident. The permanent guard that keeps it
+  # true is the L0 gate conformance/tests/l0-static/flux-postbuild-substitution/.
+  #
+  # NOTE the gate does NOT catch default-providing forms (`${VAR:-d}`, `${VAR:?msg}`, `${VAR:=v}`) —
+  # Flux exempts them by design. That class is what the L0 gate covers; the two are complementary.
+  #
+  # This also pre-pays for the Flux 2.4.0 -> 2.9.x upgrade: strict substitution became DEFAULT-ON in
+  # kustomize-controller v1.9.0, so the upgrade flips this behaviour whether or not we opt in.
+  #
+  # JSON-6902 `add ... /args/-` (append), NOT a strategic merge: a container's `args` is an atomic
+  # list, so a strategic-merge patch would REPLACE every arg `flux install` generates
+  # (--events-addr, --watch-all-namespaces, --log-level, --log-encoding, --enable-leader-election)
+  # and silently drop any the CLI adds in a future version.
+  - target:
+      group: apps
+      version: v1
+      kind: Deployment
+      name: kustomize-controller
+      namespace: flux-system
+    patch: |-
+      - op: add
+        path: /spec/template/spec/containers/0/args/-
+        value: --feature-gates=StrictPostBuildSubstitutions=true