Check out the SQL Server Database Project offered within SQL Server Data Tools. The Database Project supports managing the properties of a database (e.g. things like the recovery mode and settings like AUTO_CREATE_STATISTICS) together with the database schema and objects within that database. It will not handle some things like Replication or Log Shipping that challenge the line between database and instance configurations, although you can still incorporate the creation of some instance level objects (e.g. Linked Servers) into a database project that models the master database.

A starter video:

Build SQL Server databases using SSDT without leaving Visual Studio

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