Nonkube directory tree enhanced for documentation

[fgiorgetti]

The non-kube directory tree has been updated, so that the files are placed in more appropriate locations, with the intention to make it simpler and more cohesive to explain and to document.

Here is a brief overview of the new tree under the default namespace:

./default/
├── input
│   ├── certs
│   └── resources
├── internal
│   ├── scripts
│   └── snapshot
└── runtime
    ├── certs
    ├── links
    ├── resources
    └── router

Fixes #1759