Can't solve 2 pretty much basic usability problems

Hello everyone!

Having some trouble with non-existant project that wants to be opened at the startup, but the directory doesn’t exist anymore. There’s a yellow windows telling me that every time I’m starting Atom. I just cannot see how that project is removed?

And the second problem is that Atom keep opening files at the startup, even if I closed them. Can it remember the last session and open it on the startup?

Thanks!

Deleted missing project from ./atom/storage/application.json file, and there’s no more missing project warning and it retains open tabs through sessions.