Grouping by process-type: squashed version

Created by: RosalynLP

This is the branch with the squashed version of the changes made just on the grouping by process type branch, where I have cherry-picked the relevant commits. It replaces the PR #204 and hopefully should be clearer to read.

Note that all the diag covmats functions are "deleted" - this is because they were added from a separate branch to master, but did not appear on the old proc2 branch. When merging into master hopefully we should recover these diag_covmat functions from master.

@Zaharid does this look OK to you?