Why is atom sometimes showing every file on my desk top?

I am not sure if this is the place to ask this question but I’ve run into this problem, When I open atom it has my desktop folder loaded in. I can’t delete it. I just want it to open fresh and void of files.

Right-click on the text Desktop and select Remove Project Folder.

Atom’s current behavior (the default will change in a future release) is to automatically add as a project folder the directory of any file you open, and it looks like you opened the index.html you have on your desktop. The best immediate fix for this would be to move all code files into their own folder.