Unless I’m missing something the git status indication in the sidebar and statusbar as introduced in build 3181 only works when the repository is in the root of the sidebar. Most of my repositories however are under one top directory and that is the one which I have in the sidebar, and the git status isnt shown on any of the subdirectories. Here’s an example, Repo1 resides under TopDir, but only when added directly under Folders it’s shown as a git repository:
It would be great if Sublime would consider nested directories as well.