If you cannot create / run a project, choosing a new release due to the lack of a file, you need to add it to the original control.
Yes, this is a binary file, and you cannot distinguish it, but as the column names change over time, your code must change to work with this scheme. It makes sense to store everything in the original control, since they must match.
If you really can not pass it to the source control in the form of binary code, then consider writing it when creating an application for the database at startup, if there is no db. The following tool will interact in the sql management studio to include scripts.
http://exportsqlce.codeplex.com/
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