Fix directories in Doxyfile
After working with RTD with the recent doc-related MRs I discovered the API documentation was not building properly. This MR fixes the issue.
- Replace old src/amdis/... paths with amdis/... in Doxyfile
- Build doc for all backends, not just MTL
- Split howto.md into two files and include them in doc
- Hide Dune namespace from doc (contains almost only forward decl)