This question hasn’t been asked before, which probably means I’m missing something.
I see the squirrel icon which says, “An update will be installed the next time Atom is relaunched. Click the squirrel icon for more information.”
Is there an option somewhere which will restart Atom for me? If I wait until a package updates, a button will pop up which says, “Restart and Install Update.” Is there a way to restart Atom besides this button?
Thank you! I think I see the problem now. When I click the icon, it says Atom is already up to date.
It must just be a temporary bug?
Probably, yes. It should clear up on the next update at the latest. If it doesn’t let us know 
Hi, I can not find where the squirrel icon is, I’m using ubuntu 16.10 gnome 3.22.2 session. Is that only available on MacOs?
Squirrel is only available for OS X and Windows, yes. Linux users have to update manually (though it’s possible to install a package that can notify you when a new update comes out).
Thanks for reply,
What I want to do is restart atom in Linux like clicking on restart button which comes after update a package. Is it possible? I mean restart, not reload.
You can use the console or a custom command to invoke the atom.restartApplication() function.
Can you explain a little bit more about that. I used [atom --help] and it does not have any option like restart. I have taken a look at that function, Is it possible to create a button to execute that function on atom?
By console, I meant the JavaScript debugging console, which is accessible via View -> Developer -> Toggle Developer Tools. You can type in atom.restartApplication() and it will restart. Creating a command is easy through the init.coffee file and the CommandRegistry API:
atom.commands.add 'atom-workspace', 'user:restart', ->
atom.restartApplication()
Then you can use a package like flex-tool-bar to create a button if you want.