Open an Atom window and add a project folder. There you go. You can create whatever files you want. Atom will not do anything for you or hold your hand, because Atom is not a Java-specific editor and it doesn’t have any opinions about what files you should create or how you should structure your files. That’s all up to you.
Compile and Run a Project
Debug and Breakpoints
I don’t see any packages specifically for debugging Java, but I assume the compiler has that functionality built in.