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Hi Jeff,
Great questions.
We try to deal with complex situations as simple as possible, but complex things can get complex. So, of course, "it depends".
We're starting to document some of these in our specifics section ( http://inedo.com/specifics ) -- it's a work in progress, but we hope it gives some idea.
The first step is to "translate" your organizational specific terminology to BuildMaster's terminology. We model software development as a whole, so we can implement really any structure process... it's just about figuring out what should be a deployable, what should be an application, etc. The "Release Management Done Right" whitepaper discusses the terminology we use.
With only the information you provided, it's difficult to give specific advice, but from what it sounds like, the question is between Applications and Deployables. There's a KB article on the topic - http://inedo.com/support/kb/1032/the-difference-between-deployables-and-applications - that discusses differences.
Dependencies are defined at the deployable level (AppX depends on EntFramework) and used at the release level (AppX 3.2 depends on EntFramework 2.0). This enables all sorts of complex patterns we've seen implemented.
Feel free to contact us ( http://inedo.com/contact ), and we can discuss this in more detail and possibly help build a proof of concept.
Best,
Alex