V2 update nonkube directory tree

[fgiorgetti]

Is your feature request related to a problem? Please describe.
Update V2 nonkube directory tree to make it simpler to comprehend and document.

Describe the solution you'd like
Here is the suggested tree:

[public]
input/resources (read write)
input/certs/{ca,client,server} (read write)
runtime/resources (read only)
runtime/links (read only)
runtime/certs/{ca,client,server} (read only)
runtime/router (read only)

[internal]
internal/scripts
internal/snapshot

Additional context
Add any other context or screenshots about the feature request here.