As it turns out this is very simple. In the Database project add a reference to the SqlClr project. The database project will then automatically identify the assembly, and add it to it's set of scripts.
With the assembly added to to the database, it's a simple matter to reference it in the create scripts of the CLR types, functions, aggregates, etc.
Step by step to adda SQLCLR aggregate function:
1) right-click the database project -> Add Reference.
Select the SQL CLR project from the list of projects in the solution
2) Switch to the database Schema (View -> Database Schema View)
Verify that the Assembly appears in the Assemblies foler
3) Drill down to the Functions Folder (Schema -> dbo -> Programmability -> Functions)
Right click and Add -> Function -> Aggregate Function
Edit the template accordingly to create the aggregate.
Now the database project is the a complete unit of deployment and the SQL CLR project is not needed as part of the deployment.