Rotate MPCD geometry and force coordinates

[mphoward]

Description

This PR rotates the coordinate systems of some geometries and forces to be in the (x,y) plane rather than (x,z) plane. It mostly involved replacing "z" with "y" in a bunch of places.

This PR should be merged after #1712.

Motivation and context

As explained in #662, the use of (x,z) was a legacy choice from a previous code, but it prevented possible reuse of code for 2d MPCD simulations in HOOMD, which are in the (x,y) plane, if we ever wanted to be able to do this.

Resolves #662

How has this been tested?

Existing tests have been updated by exchanging y and z coordinates as needed.

Change log

N/A

Checklist:

• [X] I have reviewed the Contributor Guidelines.
• [X] I agree with the terms of the HOOMD-blue Contributor Agreement.
• [X] My name is on the list of contributors (sphinx-doc/credits.rst) in the pull request source branch.

[github-actions[bot]]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[mphoward]

Not stale

[mphoward]

This PR is ready for review. It is the second to last C++ refactoring (one more will be completed related to #772), so getting it merged quickly would be great so that we can focus on finalizing the Python API where most of the user changes are happening.