Modularization and cleanup

[altheaden]

This PR pulls out some common code that will be used between run.serial and run.parallel. I also took the chance to do a bit of cleanup and renaming for general clarity in run.serial.

Checklist

• [x] Developer's Guide has been updated
• [x] API documentation in the Developer's Guide (api.md) has any new or modified class, method and/or functions listed
• [x] Documentation has been built locally and changes look as expected
• [x] Testing comment in the PR documents testing used to verify the changes

[altheaden]

I tested this with the PR suite against a baseline, and everything looked as expected.

[altheaden]

I am going to update the API documentation and build everything to make sure it looks okay, and then this PR will be ready for review.

[altheaden]

Everything looks good to me in the docs, so I will go ahead and mark this as ready for review.