flux bootstrap disables GPG commit verification

[fl42]

Describe the bug

I enabled GPG commit verification by adding verify to the default GitRepository in gotk-sync.yaml:

apiVersion: source.toolkit.fluxcd.io/v1beta1
kind: GitRepository
metadata:
  name: flux-system
  namespace: flux-system
spec:
  interval: 1h0m0s
  ref:
    branch: master
  secretRef:
    name: flux-system
  url: ssh://xxx
  verify:
    mode: head
    secretRef:
      name: flux-gpg-pubkeys

It works as expected.

However running flux bootstrap again (should be idempotent) removes the verify part.

⚠️ That may be considered as a security risk as users may not be aware that GPG commit verification is disabled when running flux bootstrap (e.g., on upgrade)

To Reproduce

1. Run flux bootstrap
2. Add flux-gpg-pubkeys Secret (if needed)
3. Add verify key to GitRepository object in gotk-sync.yaml

verify:
  mode: head
  secretRef:
    name: flux-gpg-pubkeys

4. Run

kubectl -n flux-system get gitrepositories.source.toolkit.fluxcd.io flux-system -o yaml

✔️ verify key is present
5. Run flux bootstrap again
6. Run

kubectl -n flux-system get gitrepositories.source.toolkit.fluxcd.io flux-system -o yaml

⚠️ verify key is not present anymore (you may also check commit issued by flux)

Expected behavior

GPG commit verification should not be disabled on flux bootstrap.
At least a strong warning message should be raised.
Ideally a --verify parameter to configure GPG commit verification should be added to flux CLI.

Additional context

• Kubernetes version: 1.21.1
• Git provider: 0.16.1
• Container registry provider: N/A

Below please provide the output of the following commands:

flux --version
flux version 0.16.1

flux check
► checking prerequisites
✔ kubectl 1.20.4 >=1.18.0-0
✔ Kubernetes 1.21.1 >=1.16.0-0
► checking controllers
✔ helm-controller: deployment ready
► ghcr.io/fluxcd/helm-controller:v0.11.1
✔ image-automation-controller: deployment ready
► ghcr.io/fluxcd/image-automation-controller:v0.14.0
✔ image-reflector-controller: deployment ready
► ghcr.io/fluxcd/image-reflector-controller:v0.11.0
✔ kustomize-controller: deployment ready
► ghcr.io/fluxcd/kustomize-controller:v0.13.2
✔ notification-controller: deployment ready
► ghcr.io/fluxcd/notification-controller:v0.15.0
✔ source-controller: deployment ready
► ghcr.io/fluxcd/source-controller:v0.15.3
✔ all checks passed

[hiddeco]

If you patch your resources as described in https://fluxcd.io/docs/installation/#customize-flux-manifests this should not happen.

[fl42]

Thanks for the point, it works.
I wrote a small guide to help future users

[fl42]

However should I let this issue open until a warning message is issued if flux bootstrap erases user customization?

[stefanprodan]

We've added a warning to the sync manifests in #2050, closing this.