Add a few sequence diagrams to Doxygen docs.

- Add detection for mscgen to be used with Doxygen.  If the tool is not
  found, the diagrams are simply not generated (missing images on the
  HTML pages).
- Add a separate wrapper script for running Doxygen to show warnings
  more clearly (in particular errors from mscgen were difficult to spot
  otherwise).  This script also prints a note if mscgen is not available
  when the documentation is built.
- Add a few sequence diagrams for the analysis framework to clarify
  interactions between parts and illustrate the parallelization design
  (although parallelization itself isn't implemented yet, it is useful
  to see the plan to fully understand the design).  Added some text to
  describe the diagrams; this could perhaps be better integrated into
  the other documentation (currently, more or less the same text may
  also be found elsewhere).
- Fix a few Doxygen issues (missing links etc.) noticed while adding the
  diagrams.

Change-Id: If26049560b8db3be1e202d0aef6e08f0db7d5e73