I've been a long time user of Source tree. And often used it to stage and unstage files from working directory. 

I've recently reinstalled my OS and all my software, and now I find that I can't use sourcetree to stage or unstage files. The checkboxes for file staged and unstaged in source tree seem to do nothing. They don't seem to reflect what is actually staged in the index in git. i.e. git and source tree seem to work completely independently and don't share the index.

I've been watching this bug for a week or so now. I've experienced it on every repo I work with.

git version is 2.13.3

sourcetree is 2.6 (123)

MacOS Sierra 10.12.6

I've attached screenshots showing SourceTree and git, disagreeing on what is staged.