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New file tree APIs in Brackets 0.44
Brackets release 0.44 is in prerelease right now. That means we're just a few days away from release.
I don't know that this extension will continue to work after 0.44 is released. Specifically, the new file tree is based on React and React is sensitive to its DOM being manipulated without its knowledge. We have a new API that lets you add classes to the file tree nodes. I think that new API will work for you. You'll just need to change your selectors to reach the extension underneath the LI with the class you want.
Take a look at the addClasses provider for brackets-git that I wrote as an example.
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