Hello there!
I’m a happy Atom user for webdev stuff, and recently started using Atom Platformio IDE for my ESP8266 projects…
The problem is that the toolchain I have under Atom doesn’t play well with Atom Platformio IDE, and since both share the same ~/.atom storage, it’s easy to break everything, really easy…
I’m often in a situation where, to do regular work, I must disable the Platformio IDE pluging from my regular Atom, and, re-download the whole Atom Platformio IDE when I want to do ESP/*duino stuff because I can’t just re-enable it’s plugins under the Atom Platformio IDE… (If you do so, various things will break…)
And before you ask, I tried all plugins switching/enablers, the same issue happen with all of them.
Remember, they share the same storage under ~/.atom, so, installing Atom Platformio IDE means the plugins will be written to ~/.atom/ and thus pollute the regular Atom installed…
So, to avoid this, I think a split between the storage used by regular Atom and the storage used by Atom Platformio IDE seems inevitable…
Therefore, is it possible to tell Atom Platformio IDE to use another storage dir than ~/.atom ?
My research in that area were less than successful for now… But maybe some of you know?
Many thanks for your time reading these lines 
Best regards.