Replicate folder structure option for generate-ref script

**I'm submitting a...**

- [ ] Bug report.
- [x] Feature request.

## Feature request ##

Concepts of namespaces don't exist in GDScript, however, it's useful in an API reference to have sections separated by themes or namespaces, for specific areas of the API.

The generate-ref script could benefit from a "replicate folder structure" option, where the project's folder structure is replicated inside generated docs. It would allow large codebases API to be structured in the same way and be easier to navigate. Specifying a max-depth could also be useful, as one could just want to sort API docs by top-level folder structure.