There is currently no good support in VS for database developers for managing link data.
There is a good posting on MSDN that suggests using this missing feature, which uses a temporary table and a post-deployment script to merge changes into reference data during deployment.
Essentially, your referenced data exists as a static set of insert statements in your temporary table, and then the merge keeps the current tables up to date.
I have used this approach in a large CI full project for the last five months or so and found that it works well.
I also crossed my fingers that they would add better support for this in VSDB vNext.