GitHub Tree View Integration

I just started using GitHub, and I learned about this super cool feature Atom has, where it color codes your files orange, green, red for modified, new, and deleted, respectively. I think it’s a very useful feature, but it also distracts me when I can’t turn them all to white. I thought as long as I add everything to git and commit, files in the tree-view should turn white. But it seems that’s not the case. See the picture! My local repo is up-to-date, but Atom still shows files as modified. Why does Atom think these files are modified? How can I ensure a consistency between git status and what Atom shows?

Disclaimer: I know very little about all this as I’m new, so it’s possible that everything is right, and I just don’t understand what I need to do.

tempsnip

Fixed
It turns out due to different line endings in Linux (WLS which I’m using) and Windows (on which Atom is running), changes made from one system makes the other system flag the file as modified. To put a stop to this negative feedback loop, we need to ignore file mode changes:
git config core.fileMode false.

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