Doxygen: audit codebase to make documentation consistent

[rfairley]

Describe the feature
This adds documentation as comments to functions, classes, namespaces, files, etc. throughout the code using doxygen macros.

Remove unit tests from documentation (as discussed today).

Relevant items from (#121):

Remove names after @file in Doxygen
Reason: Apparently we do not actually need any name after this tag, so we should just remove it using a script

Reason for request
Consistently document the codebase fully so it can be read nicely in the rendered documentation. Also allows us to "catch up" where

Timeline
Merge before next "release" in first week of Feb.

[rfairley]

Some of this was done in #193