My kubernetes manifests are organized into two main folders:
- apps
- flux
The apps folder contains all the actual manifests for all the different apps I'm running in my cluster. The subfolder structure is organized per namespace. I try to organize apps into namespaces that makes sense. While some namespaces only have a single deployment, e.g. rook-ceph or cert-manager. Most namespaces group similar apps.
The 'flux' folder contains top level flux kustomizations that point to the manifests in apps and to a subfolder where I keep my helm resources. The components subfolder contains manifests that are deployed in more than one namespace. Keeping them here lets me define them only once and reference them where I need them.