manual: try to integrate the doxygen text a bit better

We should have a readable manual at all times, even when its not
particularly complete. Do a quick pass to remove the FIXMEs caused by
the moving of doxygen text into the manual.
dia to sml: fix logger name in comments parser
dia to sml: Move dia tags into dia_to_sml model

- renamed these tags in keeping with scoped structure and lower-cased
  them
- fix the fallout across all models, test files etc.
manual: add section on dia tags