Atom editor no longer opens from command line
Looks to me as though it's running 

/Applications/Atom.app/Contents/Resources/app/atom.sh 

but you should be able to edit your ~/.bash_config and add the line 

alias atom="/Applications/Atom.app/Contents/MacOS/Atom" 
then re-open terminal and you'll be able to launch atom by typing atom [filename], assuming your copy of Atom is installed in the /Applications folder