Have left comment on #3.
this error is back for me.
When trying to upload I get the FILE isn't part of sketch error.
The FILE is part of sketch, really.
All packages updated.
OSX 10.10.5 Yosemite
ATOM 1.23.3
Package 1.3.2
PATH = /Applications/Arduino.app (note .app required on my system).
Error from command line as well as drop down.