[FIX] Move substitute files into a tmpl folder

Cleans up `envsubst` command and allows command to be re-run

cluster/base/flux-system/gotk-sync.yaml

@@ -1,31 +0,0 @@
----
-apiVersion: source.toolkit.fluxcd.io/v1beta1
-kind: GitRepository
-metadata:
-  name: flux-system
-  namespace: flux-system
-spec:
-  interval: 1m0s
-  ref:
-    branch: main
-  secretRef:
-    name: flux-system
-  url: ssh://git@github.com/$BOOTSTRAP_GITHUB_REPOSITORY
----
-apiVersion: kustomize.toolkit.fluxcd.io/v1beta1
-kind: Kustomization
-metadata:
-  name: flux-system
-  namespace: flux-system
-spec:
-  interval: 10m0s
-  path: ./cluster/base
-  prune: true
-  sourceRef:
-    kind: GitRepository
-    name: flux-system
-  validation: client
-  decryption:
-    provider: sops
-    secretRef:
-      name: sops-gpg