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    <p>The way I understand your description, you have two problems:</p> <ol> <li>A project reference from project A to project B is broken when the projects are instantiated</li> <li>A reference to a dll is broken when the project is instantiated</li> </ol> <p>I'm also having problems with 1), and haven't found a way to solve that yet.</p> <p>For 2) you must make sure that the dll you are referencing is part of the project itself, and is listed in the project's content in your vstemplate metadata file.</p> <p>See for instance my template for F# and XNA: In the .fsproj file (similar to a .csproj for a C# project):</p> <pre><code> &lt;ItemGroup&gt; &lt;Reference Include="FSharp.Core"&gt; &lt;HintPath&gt;Dependencies\FSharp.Core.dll&lt;/HintPath&gt; &lt;/Reference&gt; &lt;/ItemGroup&gt; &lt;ItemGroup&gt; &lt;None Include="Dependencies\FSharp.Core.dll"/&gt; &lt;None Include="Dependencies\FSharp.Core.xml"/&gt; &lt;None Include="Dependencies\FSharp.Core.sigdata"/&gt; &lt;None Include="Dependencies\FSharp.Core.optdata"/&gt; &lt;/ItemGroup&gt; </code></pre> <p>In the .vstemplate file:</p> <pre><code> &lt;Folder Name="Dependencies" TargetFolderName="Dependencies"&gt; &lt;ProjectItem ReplaceParameters="false" TargetFileName="FSharp.Core.dll"&gt;FSharp.Core.dll&lt;/ProjectItem&gt; &lt;ProjectItem ReplaceParameters="false" TargetFileName="FSharp.Core.xml"&gt;FSharp.Core.xml&lt;/ProjectItem&gt; &lt;ProjectItem ReplaceParameters="false" TargetFileName="FSharp.Core.optdata"&gt;FSharp.Core.optdata&lt;/ProjectItem&gt; &lt;ProjectItem ReplaceParameters="false" TargetFileName="FSharp.Core.sigdata"&gt;FSharp.Core.sigdata&lt;/ProjectItem&gt; &lt;/Folder&gt; </code></pre> <p>See also <a href="https://stackoverflow.com/questions/1343857/visual-studio-project-template-and-private-assembly-referencing">Visual Studio Project Template and Private Assembly Referencing</a> for an alternative solution if you don't want to include the dll in your template.</p>
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