I just started using Atom and I really like some of the features, especially the PHP debugger that you can install. I have atom-beautify installed and maybe I have it installed wrong or have some conflicts with other packages because it doesn’t seem to work that well. White space and extra lines are left alone, and it doesn’t even really format the code that well. It is mixed PHP and HTML. Is there some trick to getting it to work well ? Conflicts with other extensions. I have php-fmt and the css module installed.
You may want to follow up with the maintainer of the atom-beautify package. The Atom FAQ has information on how to contact the maintainers of any Atom community package or theme.