Misc. Doxygen improvements.

Misc. Doxygen improvements.

- Excluded src/external/ from Doxygen documentation.
- Made inherited members appear in class documentation. Makes API
  documentation easier to read if there are many public members
  inherited from base classes.
- Added conditional sections for Doxygen that can be used in addition to
  \internal and \libinternal.
- Consolidated use of \internal and \libinternal in file comments:
  all installed (=public API) headers now produce some documentation for
  the public API, even if the file only contains declarations that are
  not directly in the public API.
- Added short file documentation for a few files where it was missing.

Gromacs wiki has also been updated with the changes.

Related to IssueIDs #638 and #662.

Change-Id: I9ffb9d68752697b5b58a3cc4ae45d802e32cf45c