I don’t really like using merge, it clutters the history of my own changes with the engine commits.
So instead I just create a new branch from the new version, cherry pick over all of my commits that are still relevant, and get rid of the old branch if it works.
That’s also helpful if you added stuff to fix engine bugs, that isn’t necessary in a new version anymore.
Also you should use a tool like SmartGit instead of trying to work with the command line.