There's been a lot of what I see as confusion about the modules and components in the Atmel Studio environment. I guess that stems from the lack of information, but I have good news!
During the recent Jenkins CI User Event in Copenhagen we at the Atmel Tools Departement were asked to co-present a project that we have been working on regading CI, git and a new 'branchy' workflow.
Presentation is available for download on the Github page.
There's a lot of git and CI in it for those interested, but there's also a high-level component view of the Atmel Studio ecosystem.