As a user who uses a dotfile management system such as RCM , I prefer independent configuration files.
Atom currently does not officially provide the packages.cson file for managing plugins, but as the post Sync settings and packages between machines mentioned, there is a plugin called package-sync that will generate the packages.cson file for us.
So, with package-sync, now I can just sync these mini configuration files so that my Atom settings and packages are consistent across multiple machines.
Here's how to do it (use ubuntu as an example):
- Install Atom and install package-sync via Edit β Preferences β Install as the screen shows:

Open the control panel and type: Create Package List and ~/.atom will be packages.cson in the ~/.atom folder.

Edit the gitignore file:
$ gedit ~ / .atom / .gitignore
Make sure the content:
blob-store compile-cache dev storage .node-gyp .npm .apm packages/ atom-shell/
This is a screenshot of the .gitignore file: 
This ensures that content downloaded by Atom from the Internet is not synchronized with your dotfiles replica.
Move the .atom folder to the .atom repository:
$ mv ~ / .atom ~ / dotfiles / tag-atom / atom
Restart the folder:
$ ln -s ~ / dotfiles / tag-atom / atom ~ / .atom
Or if you have rcm installed:
$ rcup
Now go to another machine and install Atom and batch synchronization. Update the dotfiles repository and then open the Atom control panel and type: sync
Now your Atom settings will be synchronized and integrated with the dotilfe RCM control system.
These are the files in my ~/.atom that are syncing: 
Hustlion Jul 09 '16 at 6:35 2016-07-09 06:35
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