Actually, if Atom could set JULIA_PROJECT environment variable to a predefined value for me, then that would in turn use @ in Base.LOAD_PATH point to my project.
I found this post Activate project in Juno/Atom - #2 by pfitzseb that is about the very same thing. That topic was opened more than a year ago. There must already be a way to do this, just I can’t find it.
There is a workaround that actually works: open a shell, set JULIA_PROJECT env there, and start atom from that environment. It kind of works, but it makes switching projects from Atom impossible.