You will need to set up each of the plugin folders as a git repository (this is a one-off thing).
If you have not installed the plugins yet, you can use the commands in https://github.com/maths/moodle-qtype_stack/blob/master/doc/en/Installation/index.md#3-add-some-additional-question-behaviours, like
git clone git://github.com/maths/moodle-qtype_stack.git question/type/stack
To get a specific version, you can change that to something like
git clone -b v4.2 git://github.com/maths/moodle-qtype_stack.git question/type/stack
If you do this version, then for reasons I won't try to explain here, you should then do
cd question/type/stack git checkout -b masterIf you already have a question/type/stack folder in your install. Well, one option is to just delete it then do a git clone. That is simplest. It is also possible to do it without deleting the folder, if you know enough git. (git init; git remote add ...; git fetch; git checkout ...) but there is no real reason do to that.
As Chris says, you need to do it for all the plugins (qtype_stack and the three behaviours it uses).
Once that is done, the upgrading should be as simple as going into the folder for each folder, and doing
git merge --ff-only v4.3
where v4.3 is whatever tag you want to update to. The --ff-only argument is not strictly necessary, and I am not going to try to explain it, but I think it is a good idea to avoid certain mistakes that are otherwise easy to make.