So for better or worse we've got two database projects that have essentially the same schema. The only differences being that Database 2 has a few more indexes than Database 1. Is there an easy way to keep those two projects in synch on the schema but still have those extra indexes in the Database 2 project? I essentially only want to keep the differences in the Database 2 project. The problem is trying to keep the projects in synch when making schema changes. I don't want to make the changes in two places.
Composite projects would probably be your best bet if the only change is the extra indexes. You could make your main project then base your second project on that and add the indexes. Jamie Thomson blogged about this here: http://sqlblog.com/blogs/jamie_thomson/archive/2013/03/10/deployment-of-client-specific-database-code-using-ssdt.aspx
Alternatively, you could use post-deploy scripts and SQLCMD variables to only push those indexes to Database 2. It's not as straightforward as the composite project, but could work in your situation.