Yeah, it's used as it contains the DLLs for Entity Framework, System.Web.Optimization and others.
Using the one from the source folder might work, but it depends on the versions. You may have newer versions referenced in your web.config which means you should either manually update your web.config, or use the one from the source as well.
Depending on how you installed everything, restoring the NuGet packages and recompiling may solve the problem as well.
Cheers,
Imar
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