An IDE really doesn't seem like the appropriate place for material design to me, the white-space is way overkill.
The tabs in particular are wasting tons of vertical space and unnecessary for a non-touch UI. The target market for Atom will either be accurate with a mouse/trackpad or using ⌘+P for selecting files.
Of course, I have a strong preference towards a compact and efficient layout for Atom, this is the style I'm using: http://i.imgur.com/FqcPk9l.png
The top left logo also changes based on the active project.
Thank your for your feedback!
It is and has always been a tightrope walk to balance between "wasting" space and simply making it look great to the eye. I think we can both agree on that this is not something which can be argued about, since everybody has a different taste in terms of good design.
As far as I know, Google's Material Design hasn't been created specially for touch devices. It's just a guide on how to create awesome looking interfaces on all kinds of screen sizes (they're using it everywhere on the web and even in their Desktop OS).
In terms of keeping a layout compact, I'm definitely agreeing with you. But as I already said: It's always a balancing act.