Document more of VCL's Application class

* Documented the Application class's settings functions. When
  reading through the code, I have noticed that GetSettings
  intializes the application settings (!) and that SetSettings
  relies on GetSettings to initialize the settings (!), so I
  have listed a todo entry.

  Furthermore, I've also noticed that SetSystemSettings and
  MergeSystemSettings may be confused with the purpose of
  SetSettings so I've added a todo entry that recommends that
  we return an AllSettings object and make the parameters const.

* Minor whitespace changes

* Update @see for a number of public functions

* Group functions into Doxygen modules
Change-Id: I48f8d21a5d6436a2ae545e5156b877d57a8bc585