PyCue should not pass any protobuf objects

**Describe the enhancement**
Right now PyCue uses and expects a mix of protobuf objects and wrapper objects. This is confusing to use as an api since it's not clear when to use the protobuf object vs the wrapper. Once #337 is in place we should standardize on only passing and returning the wrapper objects.

**Screenshots**
None

**Version Number**
0.2.31

**Additional context**
Dependent on #337

Start by reviewing the PyCue API and the dependent #337 change to understand the wrapper objects and protobuf objects currently exposed. Trace the public paths that pass or return each kind of object, then verify that the completed work consistently uses wrapper objects only and no longer exposes protobuf objects.

Written by the indexing model from the issue text.