Docstring updates

This updates the doc strings in a few places to be consistent with the actual parameters. I also changed Doxygen settings to improve that a little, e.g. to include the public API header.

Based on #919, #920.

coverage: 98.784%. remained the same when pulling 51df30a587bbe9e5b6705d8e9a8267f3b20b4d46 on isaacbrodsky:compact_all_res1_tes-docs into ae3117738d89e74594926c0f7c8b29a4b84d114d on uber:master.

This should be ready for review now.