You can only avoid having your constant call backs to google analytics or atom.io servers described as something other than spyware when you ask the user first if they would like you to turn on these features.

Your access to google analytics should only be enabled with the "send anonymous statistics to improve product" button, as most half decent non-spyware applications do.

Your access to atom.io to check for updates should only be enabled with the "automatically check for updates on startup" button, as is done by most reasonably sane applications.

Asking users to edit your coffee script in order to disable is not a valid response.