I have been using Atom for a few months now, however it is not without faults.
I use Nuclide packages from Facebook as a lot of my day to day work is now written in Hack rather then PHP.
Atom it self is quite hackable and visually appealing, it has gained a massive range of packages quickly and adding your own is easy with some basic JS experience.
However to get the best you need to spend time configuring and installing a lot of packages.
@kingkool68 - https://atom.io/packages/project-manager might be useful for you
Which then leads to the biggest issue, it's insane memory hog (1.2gb of RAM with 10 tabs open) and it make Eclipse look like a lean efficient IDE sometimes in comparison.
To put in perspective on my MacBook Pro 2010 to open a file from close you are looking at:
20secs for Sublime
45secs for Eclipse
55secs for Atom
To a point where you can start editing.
You will also find the joys of...
Which is a regular occurrence along with packages (including core ones) crashing regularly.
So why use it if it's slow and buggy?
I really have limited choice nuclide is the only IDE to fully support Hack. One question I get is it, just the packages and Nuclide in particular causing the issues, without any community packages, the open time is around 50 seconds so having 20 packages installed is adding about 5 seconds to load, stability wise it's about the same.