How do I turn off ALTER DATABASE script output in VS 2012?
I am using Visual Studio 2010 and SQL 2008 database projects, but the idea remains the same.
In your solution go to the project and do the following steps:


right click the project -> Properties
Project Settings (1st tab in this setting)
go to section Catalog Properties file: make sure a settings file is already selected (by default there's a file \Properties\Database.sqlsettings if it wasn't previously changed)
click Edit for the sqlsettings file: there you'll see all the options that are deployed each time to your target database. It should look like the following snap:



If you'd like to NOT deploy any of the project default settings, you should do the following steps:


go to tab Deploy
go to section Deployment configuration file (default it is Properties\Database.sqldeployment)
deselect the option "Deploy database properties". It should look something like the following snap:



That should help you change/remove the current project settings that you're now deploying.