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This is probably caused by migration scripts: when you create a migration script, SQL Source Control captures the state of any dependent objects. The "old" assembly is probably being created because of that.
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So if I where to "edit & save" the dependant scripted would that help?
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In theory yes, however in practice we have seen that some times dependency changes aren't picked correctly when a script is edited.
If you don't need any of the migration scripts anymore, you can quickly resolve this by just emptying the "Custom Scripts" subfolder in your repository (however please note that you can't individual migration scripts this way: it's all or nothing).
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We have hit a small issue, we are adding a Assembly to our next version. During development updated the Assembly after some other Database changes where made. Now when we compare an old db with the current source control version we get the Assembly included twice (i assume the original and the update version) at different points in the updates script. Is there a way to only have the current version included?