As of July 30th, 2010:
B&I builds two projects for the MobileNotes project.
MobileNotes - builds the NotesApp target
MobileNotesFramework - builds the Notes target
The search bundle and data migrator are listed as direct dependencies of the NotesApp target, not because they actually are in terms of the code, but because they need to get built by B&I.
IMPORTANT: Purple itself does not get built in B&I, which is a bit counterintuitive.

We absolutely cannot have the Notes target be a direct dependency of the NotesApp target.  The original reason for this was that it creates a circular dependency:
Search -> Message -> DataAccess -> Sync -> MobileNotes -> Search

However, we accidentally changed that once, and it didn't cause a massive build failure, but it did cause this:

<rdar://problem/8240228> Can't debug using Jasper8C60 / 8C61 (UUID mismatch)