My sublime text projects were folders containing git repositories. That was fine until the introduction of the git features a couple of days ago: there was no sign of the promised git integration features.
Gitgutter was still working fine, my git is in my path, and there was nothing special with my sublime text/merge installation.
So I was sad
Turns out it seems you have to add your git repositories at the top level of your projects.
An easy fix once you know it.
But maybe it would be nice to handle that case (i.e., a folder containing repositories), as it makes adding new repositories in a project seamless (you just have to create/clone your repository in that folder, and it automatically appears in the sublime text project, vs. the current situation, where you have to add it to your project).