There were some paths in the csproj that were broken:
<ItemGroup>
<Reference Include="MongoDB.Bson">
<HintPath>..\web\packages\mongocsharpdriver.1.8.3\lib\net35\MongoDB.Bson.dll</HintPath>
</Reference>
<Reference Include="MongoDB.Driver">
<HintPath>..\web\packages\mongocsharpdriver.1.8.3\lib\net35\MongoDB.Driver.dll</HintPath>
</Reference>
<Reference Include="MongoRepository.Net45, Version=1.6.2.0, Culture=neutral, processorArchitecture=MSIL">
<SpecificVersion>False</SpecificVersion>
<HintPath>..\packages\MongoRepository.1.6.3\lib\net45\MongoRepository.Net45.dll</HintPath>
</Reference>
<Reference Include="System" />
<Reference Include="System.Core" />
<Reference Include="System.Xml.Linq" />
<Reference Include="System.Data.DataSetExtensions" />
<Reference Include="Microsoft.CSharp" />
<Reference Include="System.Data" />
<Reference Include="System.Xml" />
</ItemGroup>
Needed to change the HintPath to ..\packages to remove the web directory.