Store atom-shell cache in ~/.atom/atom-shell

There were several CI failures today where it seemed like the
atom-shell version in the temp directory wasn't complete, it was
missing many files causing the build to fail when the specs were
run.

What made this worse was that running script/clean on these machines
didn't clean out these bad versions since the temp directory was different
when run via Jenkins vs. ssh'ing into the machines so the folders were
left there and the builds kept failing.

Atom already stores the compile cache to ~/.atom as well as the node cache
so putting atom-shell there as well keeps things consistent.