Create a high level directory, "nameMeWhatever".
2 .Pull multiple repos into the parent directory named "nameMeWhatever",
Open the highest level directory in Atom as a project
Your folder view on left should look like
nameMeWhatever (root directory opened as a project)->
repo1
repo2
Steps to reproduce,
Make changes in either repo1 or repo2.
See that git-diff is unable to track the changes.
Seems like a bug to me.