Clean up and fix issues in doc-check scripts

- Some 'documentation' -> 'doc' replacements in method names to make
  lines shorter and to make method names more consistent.
- Make the checker work for members of anonymous namespaces.
- To achieve the above, add minimal modeling of namespaces and members
  to gmxtree.py, and model the parent compounds of members better in
  doxygenxml.py.
- Make the checker check also documentation that is ignored by Doxygen.
  This is now possible when anonymouns namespaces work.
  --check-ignored now only controls whether the ignored comments provoke
  a note or not.  This is not enabled currently, because it produces
  quite a lot of noise.
- Fix documentation issues in those ignored Doxygen comments (all the
  source code changes).
- Encapsulate some logic in gmxtree.py related to how the API type is
  handled in the case of legacy (undocumented) modules.  This simplifies
  the graph generation logic, and replaces a lot of the "legacy" edges
  with more descriptive edges: installed headers in legacy modules are
  now treated as public API headers.
- Add a basic legend to the module graph.

Change-Id: Ia4e83468548b361f37bdb8d35862e636d7abddd6