In my current project I'm using an open source forum (https://github.com/vanillaforums/Garden.git). I was planning on doing something like this :

git remote add vanilla_remote https://github.com/vanillaforums/Garden.git
git checkout -b vanilla vanilla_remote/master
git checkout master
git read-tree --prefix=vanilla -u vanilla

This way I can make change into the vanilla folder (like changing config) and commit it to my master branch and I can also switch into my vanilla branch to fetch updates. My problem is when I try to merge the branch together

git checkout vanilla
git pull
git checkout master
git merge --squash -s subtree --no-commit vanilla

The problem is that the "update commit" goes on top of my commits and "overwrite" my change. I would rather like to have my commits replay on top of the update. Is there a simple way to do that? I'm not very good in git so maybe this is the wrong approach. Also, I really don't want to mix my history with the vanilla history.