git care and feeding
The master branch is pulled from the upstream http://git.redump.net/mame which is a (semi-sortof-official) git mirror of the mame SVN trunk. To update, make sure you have a 'mame-upstream' remote:
git remote add mame-upstream http://git.redump.net/mame
git fetch --all
then move the master branch to match:
git checkout master
git merge --ff-only mame-upstream/master
If that fails, someone committed changes to the master branch, and they will need to be saved elsewhere and the master branch rewound.
The no_cothreads branch is (at the time of writing) the primary branch of development, for historical reasons: cothreads were added to MESS, which broke jsmess. They have since been removed, but there were other challenges in pushing jsmess forward to the head of the mame upstream, mostly involving SDL2.0, that haven't yet been re-investigated. (The jsmess_trunk branch was an effort to resolve those problems, partially successful.)