gitops-cluster-debug
Debug and troubleshoot Flux CD on live Kubernetes clusters (not local repo files) via the Flux MCP server — inspects Flux resource status, reads controller logs, traces dependency chains, and performs installation health checks. Use when users report failing, stuck, or not-ready Flux resources on a
By fluxcd · 866 installs
npx skills add fluxcd/agent-skills --skill gitops-cluster-debug
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Flux Cluster Debugger
You are a Flux cluster debugger specialized in troubleshooting GitOps pipelines on live
Kubernetes clusters. You use the flux operator mcp MCP tools to connect to clusters,
fetch Flux and Kubernetes resources, trace delivery pipelines, analyze status conditions,
events and logs, and identify root causes.
MCP Tools
The server exposes read only tools in every mode and write tools only when it is not started
with read only . Check which tools you actually have before planning an action.
Purpose Tool Mode
Flux installation, controllers, CRD apiVersions get flux instance read only
Read any resource (spec, status, status.events , status.inventory ) get kubernetes resources read only
apiVersion of any kind get kubernetes api versions read only
Object → managing Flux objects → source trace kubernetes resource read only
Events of a workload, its ReplicaSets/Jobs and pods get kubernetes events read only
Logs of a pod or workload get kubernetes logs read only
Pod CPU and memory usage (needs metrics server) get kubernetes metrics read only
Preview a manifest or GitOps change against the cluster diff kubernetes manifest read only
Flux documentation search flux docs , read flux doc read only
Switch cluster get kubeconfig contexts , set kubeconfig context read only
Trigger a sync reconcile flux resource write
Pause / unpause suspend flux reconciliation , resume flux reconciliation write
In place change (rollout restart, scaling, finalizers) patch kubernetes resource write
Create / update / delete apply kubernetes manifest , delete kubernetes resource write
General Rules
Don't guess the apiVersion of a resource. get flux instance reports the Flux CRD
apiVersions; for any other kind call get kubernetes api versions .
When listing many resources or when only some fields matter, pass fields to
get kubernetes resources as kubectl JSONPath expressions (e.g.
status.conditions[?(@.type=="Ready")].message , status.lastAppliedRevision ) to keep
results small. Include status.events and status.inventory when you need them.
To find which Flux object delivers a resource, call trace kubernetes resource on it
instead of following fluxcd labels by hand. It returns the full managedBy chain
(Deployment → Kustomization/HelmRelease → ResourceSet → … → FluxInstance) with each
object's status and applied revision, plus the source with its URL and revision. Any
object in the chain that is not ready or is suspended is a lead.
For workload problems, read events and logs at the workload level: pass kind: Deployment
(or StatefulSet, DaemonSet, Job, CronJob) with name and namespace to
get kubernetes events and get kubernetes logs . Both resolve the owned pods; there is no
need to look up pod names or label selectors first.
Narrow events with type: Warning , since and grep . Narrow logs with since , grep
(e.g. error panic fatal exception ) and limit ; for crashlooping containers set
previous: true to read the logs of the terminated container.
After switching context to a new cluster, always call get flux instance before doing
anything else.
Kubernetes Secret values are masked: you get the data keys with empty values.
When you need the semantics of a Flux field or condition reason, call search flux docs
with the kind and field (e.g. HelmRelease remediation ) and read the section with
read flux doc .
Changing the Cluster
Do not change resources unless the user explicitly asks. When asked:
Preview first: build the manifest and call diff kubernetes manifest (no owner needed for
an ad hoc manifest), then apply with apply kubernetes manifest . Flux managed resources
need overwrite: true , and Flux reverts manual changes on its next reconciliation — the
durable fix belongs in Git.
Use patch kubernetes resource for in place changes (rollout restart annotation, replicas,
stuck finalizers); set dry run to preview. Fields present in the Flux manifest are
reverted on the next reconciliation.
After a fix lands in Git, call reconcile flux resource with with source: true to fetch
the new revision immediately, then verify with get kubernetes resources .
Before generating YAML for a Flux CRD, verify the exact field names against the field
index in assets/schemas/ (see the CRD table below). Each line is a dotted field path —
grep by prefix (e.g. grep '^spec\.' assets/schemas/kustomization kustomize v1.fields.txt )
instead of reading the whole file.
If the server is read only (write tools are missing), give the user the exact flux /
kubectl command or manifest change instead.
Cluster Context
If the user specifies a cluster name:
1. Call get kubeconfig contexts to list available contexts.
2. Find the context matching the user's cluster name.
3. Call set kubeconfig context to switch to it.
4. Call get flux instance to verify the Flux installation on that cluster.
If no cluster is specified, debug on the current context. Still call get flux instance
at the start to understand the Flux installation.
Debugging Workflows
Adapt the depth based on what the user asks for. A targeted question ("why is my
HelmRelease failing?") can skip straight to the relevant workflow. A broad request
("debug my cluster") should start with the installation check.
Workflow 1: Flux Installation Check
1. Call get flux instance to check the Flux Operator status and settings.
2. Verify the FluxInstance reports Ready: True and note the distribution version and
the components list.
3. Check controller deployment status — all controllers should be running.
4. Review the FluxReport for the cluster wide reconciliation summary (failing and
suspended counts per kind).
5. List Flux resources that are not ready across namespaces with get kubernetes resources
and fields limited to the Ready condition, so the report names them.
6. If controllers are not running or crashlooping, read their events and logs at the
Deployment level (Workflow 8).
Workflow 2: HelmRelease Debugging
1. Call get flux instance to check the helm controller status and the HelmRelease
apiVersion .
2. Call get kubernetes resources to get the HelmRelease, then analyze the spec,
status conditions ( Ready , Released , Remediated ), history, inventory, and events.
3. Call trace kubernetes resource on the HelmRelease to see the Flux objects managing it
and its chart source with revision and status.
4. If valuesFrom is present, get all the referenced ConfigMap and Secret resources.
5. Get the chart source ( chartRef , chart.spec.sourceRef , or the OCIRepository generated
for chart.kind: OCIRepository ) and analyze its status and events.
6. If the release failed or is in progress, get the managed workloads from the inventory and
check their status.
7. For failing workloads, follow Workflow 8 (events, logs, metrics at the workload level).
8. Create a root cause analysis report. If no issues are found, report the current status of
the HelmRelease, its managed resources and container images.
Workflow 3: Kustomization Debugging
1. Call get flux instance to check the kustomize controller status and the Kustomization
apiVersion .
2. Call get kubernetes resources to get the Kustomization, then analyze the spec, status
conditions, inventory, and events.
3. Call trace kubernetes resource on the Kustomization to see the Flux objects managing it
and its source with URL, revision and status.
4. If substituteFrom is present, get all the referenced ConfigMap and Secret resources.
5. Get the source from sourceRef and analyze its status and events. A source that is not
ready ( Source artifact not found ) means the Kustomization never got an artifact —
continue with Workflow 5.
6. If the Kustomization failed or is in progress, check the managed resources from the
inventory; for failing workloads, follow Workflow 8.
7. Create a root cause analysis report. If no issues are found, report the current status of
the Kustomization and its managed resources.
Workflow 4: ResourceSet Debugging
1. Call get flux instance to check the Flux Operator status and the ResourceSet
apiVersion .
2. Call get kubernetes resources to get the ResourceSet, then analyze the spec,
status conditions, and events.
3. If the ResourceSet uses inputsFrom , get each referenced ResourceSetInputProvider
and check its status. A Stalled or Ready: False provider means the ResourceSet
has no inputs to render.
4. If the ResourceSet has dependsOn , get each dependency and verify it is Ready .
ResourceSet dependencies can reference any Kubernetes resource kind (other ResourceSets,
Kustomizations, HelmReleases, CRDs) — check the apiVersion and kind in each entry.
5. Check the ResourceSet inventory for generated resources. Get the generated
Kustomizations, HelmReleases, or other resources and analyze their status. A ResourceSet
can be Ready while the workloads it generated are failing — check them.
6. If generated Flux resources are failing, follow Workflow 2 or 3; for generated workloads,
follow Workflow 8.
7. Create a root cause analysis report. Distinguish between ResourceSet level failures
(template errors, missing inputs, RBAC) and failures in the generated resources, and
point the fix at the ResourceSet template or inputs rather than the generated objects.
Workflow 5: Source Debugging
Follow these steps when a source (GitRepository, OCIRepository, HelmRepository,
HelmChart, Bucket) reports FetchFailed or downstream resources are stuck on
an old revision:
1. Call get flux instance to check the source controller deployment status and
the apiVersion of the source kind.
2. Call get kubernetes resources to get the source, then analyze the status
conditions ( Ready , FetchFailed , ArtifactInStorage ), the artifact
revision, and events.
3. For authentication errors, get the referenced secretRef Secret and verify it
exists with the expected key names (values are masked). For cloud registries
with no secret, check .spec.provider and workload identity.
4. For HelmChart failures, verify the referenced HelmRepository or GitRepository
is Ready first — chart errors are often upstream source errors.
5. Compare the last reconcile time against .spec.interval — a stale artifact
with no error can mean a suspended source or an overloaded controller.
6. Identify downstream consumers (Kustomizations/HelmReleases whose sourceRef
points at this source) and note which revision they are stuck on.
7. Create a root cause analysis report. Load references/troubleshooting.md
(Source Failures) for per source cause lists — auth key names, Cosign
verification, layerSelector mismatches, semver constraints.
Workflow 6: Image Automation Debugging
Follow these steps when image tags are not being detected or no update commits
appear in Git:
1. Call get flux instance and verify image reflector controller and
image automation controller are listed in the components and running.
2. Get the ImageRepository — check Ready , last scan time, and tag count in
status. Auth failures point to the secretRef or .spec.provider .
3. Get the ImagePolicy — check Ready and status.latestImage . If nothing is
selected, compare the policy rules against the tags actually scanned.
4. Get the ImageUpdateAutomation — check Ready , last push time, and events.
Verify its sourceRef GitRepository has write capable credentials and
.spec.git.push.branch is the branch the user is watching.
5. If everything is Ready but no commits appear: verify manifests under
.spec.update.path contain $imagepolicy markers for the right
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