Cherry-Pick Non-Science Changes

Cherry-picks all commits from the merge requests !8 (merged), !9 (merged), !12 (merged), !13 (merged), and !16 (merged)

There were few conflicts, all were cases where some code had been reformatted in O4-dev and changed/deleted in the old merge requests (so the incoming changes were always accepted).

The commit for !7 (merged) was excluded as the work was redone as part of the clang reformat

Still requires testing and internal review, as well as a rerun of clang format.