As Atom has matured, there have been some bumps. I have had to uninstall/reinstall due to buggy or sluggish behavior. These scripts automate most of that process.
Download Atom and install it if it is not installed.
git clone git@github.com:mattnorris/atom-install.git
make dev
If you receive an error that apm is not installed, run Atom > Install Shell Commands and try again.
Also remember to:
Based on morberg's answer to How to Completely Uninstall Atom for Mac?
make remove