Misc. Doxygen build system improvements

- Only generate the installed header list once after CMake is run.
  It cannot change unless CMake is run again.  This wasn't particularly
  slow earlier either, but now it can be added as a dependency also in
  the -fast targets without any impact on the behavior.
- Do not update the Doxyfile-common each time CMake is run if
  GMX_COMPACT_DOXYGEN=ON.
- Partition the Markdown pages into subdirectories based on the
  documentation level where they should appear.  Exclude things from
  the documentation based on the directory, not individually.
- Use a CMake function to create the various Doxygen targets to remove
  some duplication.
- Some cleanup in the directories.cpp and misc.cpp documentation files.
- Some cleanup to use consistent casing throughout CMakeLists.txt.

Change-Id: I30de6f36841f25260700ec92284762e989f66507