Further improvements to the docs

- Convert MSG and Java (not the javadoc, only generalities) to Sphinx
- Get rid of Exhale and write the doxygen directives manually.
  - I'm too picky on how things should look
  - ./Build.sh tries to check for missing directives, somehow
- Restore some doc chunks that got lost in MSG when converting to
  msg_legacy.cpp. Initially, I thought that MSG could be strongly
  deprecated, but now I understand that some people are not ready for
  the shift to S4U yet.