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    <p>The problem was the absence of the HeatDirectory PreprocessorVariable property. I fixed the issue with the following additions to my wixproj file:</p> <pre><code>&lt;PropertyGroup&gt; &lt;DefineConstants&gt;BasePath=%(ProjectReference.RootDir)%(ProjectReference.Directory);&lt;/DefineConstants&gt; &lt;/PropertyGroup&gt; &lt;HeatDirectory OutputFile="%(ProjectReference.Filename).wxs" DirectoryRefId="INSTALLFOLDER" Directory="%(ProjectReference.RootDir)%(ProjectReference.Directory)" ComponentGroupName="%(ProjectReference.Filename)_Project" SuppressCom="true" SuppressFragments="true" SuppressRegistry="true" SuppressRootDirectory="true" AutoGenerateGuids="false" GenerateGuidsNow="true" ToolPath="$(WixToolPath)" Condition="'%(ProjectReference.ContentProject)'=='True'" PreprocessorVariable="var.BasePath"/&gt; </code></pre> <p>As you can see, I needed to first define a constant variable for local use. I set the variable equal to the root path of my WCF project. Secondly I used that variable as my PreprocessorVariable. Finally I'm able to dynamically/recursively harvest the files generated from MsBuild. Next step: exclude the unnecessary files. I will refer to this <a href="http://www.chrissurfleet.co.uk/post/Using-Packaged-Project-Output-in-WiX-and-Visual-Studio.aspx" rel="noreferrer">link</a>.</p> <p>See below my complete wixproj:</p> <pre><code>&lt;?xml version="1.0" encoding="utf-8"?&gt; &lt;Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003"&gt; &lt;PropertyGroup&gt; &lt;Configuration Condition=" '$(Configuration)' == '' "&gt;Debug&lt;/Configuration&gt; &lt;Platform Condition=" '$(Platform)' == '' "&gt;x86&lt;/Platform&gt; &lt;ProductVersion&gt;3.5&lt;/ProductVersion&gt; &lt;ProjectGuid&gt;{4005592f-cc0e-41a3-8e64-33b2824e7fd9}&lt;/ProjectGuid&gt; &lt;SchemaVersion&gt;2.0&lt;/SchemaVersion&gt; &lt;OutputName&gt;MyWCF.WCF.Webservice&lt;/OutputName&gt; &lt;OutputType&gt;Package&lt;/OutputType&gt; &lt;WixTargetsPath Condition=" '$(WixTargetsPath)' == '' AND '$(MSBuildExtensionsPath32)' != '' "&gt;$(MSBuildExtensionsPath32)\Microsoft\WiX\v3.x\Wix.targets&lt;/WixTargetsPath&gt; &lt;WixTargetsPath Condition=" '$(WixTargetsPath)' == '' "&gt;$(MSBuildExtensionsPath)\Microsoft\WiX\v3.x\Wix.targets&lt;/WixTargetsPath&gt; &lt;/PropertyGroup&gt; &lt;PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x86' "&gt; &lt;OutputPath&gt;bin\$(Configuration)\&lt;/OutputPath&gt; &lt;IntermediateOutputPath&gt;obj\$(Configuration)\&lt;/IntermediateOutputPath&gt; &lt;/PropertyGroup&gt; &lt;PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|x86' "&gt; &lt;OutputPath&gt;bin\$(Configuration)\&lt;/OutputPath&gt; &lt;IntermediateOutputPath&gt;obj\$(Configuration)\&lt;/IntermediateOutputPath&gt; &lt;/PropertyGroup&gt; &lt;ItemGroup&gt; &lt;Compile Include="MyWCF.WcfService.wxs" /&gt; &lt;Compile Include="IISConfig.wxs" /&gt; &lt;Compile Include="InstallUi.wxs" /&gt; &lt;Compile Include="Product.wxs" /&gt; &lt;Compile Include="UIDialogs.wxs" /&gt; &lt;/ItemGroup&gt; &lt;ItemGroup&gt; &lt;ProjectReference Include="..\MyWCF.WcfService\MyWCF.WcfService.csproj"&gt; &lt;Name&gt;MyWCF.WcfService&lt;/Name&gt; &lt;Project&gt;{8e528b38-2826-4793-a66d-f6ff181e1139}&lt;/Project&gt; &lt;Private&gt;True&lt;/Private&gt; &lt;RefProjectOutputGroups&gt;Binaries;Content;Satellites&lt;/RefProjectOutputGroups&gt; &lt;RefTargetDir&gt;INSTALLFOLDER&lt;/RefTargetDir&gt; &lt;ContentProject&gt;True&lt;/ContentProject&gt; &lt;DoNotHarvest&gt;True&lt;/DoNotHarvest&gt; &lt;PackageThisProject&gt;True&lt;/PackageThisProject&gt; &lt;/ProjectReference&gt; &lt;/ItemGroup&gt; &lt;ItemGroup&gt; &lt;WixExtension Include="WixIIsExtension"&gt; &lt;HintPath&gt;$(WixExtDir)\WixIIsExtension.dll&lt;/HintPath&gt; &lt;Name&gt;WixIIsExtension&lt;/Name&gt; &lt;/WixExtension&gt; &lt;WixExtension Include="WixUtilExtension"&gt; &lt;HintPath&gt;$(WixExtDir)\WixUtilExtension.dll&lt;/HintPath&gt; &lt;Name&gt;WixUtilExtension&lt;/Name&gt; &lt;/WixExtension&gt; &lt;WixExtension Include="WixUIExtension"&gt; &lt;HintPath&gt;$(WixExtDir)\WixUIExtension.dll&lt;/HintPath&gt; &lt;Name&gt;WixUIExtension&lt;/Name&gt; &lt;/WixExtension&gt; &lt;WixExtension Include="WixNetFxExtension"&gt; &lt;HintPath&gt;$(WixExtDir)\WixNetFxExtension.dll&lt;/HintPath&gt; &lt;Name&gt;WixNetFxExtension&lt;/Name&gt; &lt;/WixExtension&gt; &lt;/ItemGroup&gt; &lt;ItemGroup&gt; &lt;Content Include="ConfigurationInitialize.wxi" /&gt; &lt;/ItemGroup&gt; &lt;Import Project="$(WixTargetsPath)" /&gt; &lt;PropertyGroup&gt; &lt;PreBuildEvent /&gt; &lt;/PropertyGroup&gt; &lt;Target Name="BeforeBuild"&gt; &lt;MSBuild Projects="%(ProjectReference.FullPath)" Targets="Package" Properties="Configuration=$(Configuration);Platform=$(Platform)" Condition="'%(ProjectReference.PackageThisProject)'=='True'" /&gt; &lt;PropertyGroup&gt; &lt;DefineConstants&gt;BasePath=%(ProjectReference.RootDir)%(ProjectReference.Directory)obj\$(Platform)\$(Configuration)\Package\PackageTmp\&lt;/DefineConstants&gt; &lt;/PropertyGroup&gt; &lt;HeatDirectory OutputFile="%(ProjectReference.Filename).wxs" Directory="%(ProjectReference.RootDir)%(ProjectReference.Directory)obj\$(Platform)\$(Configuration)\Package\PackageTmp" DirectoryRefId="INSTALLFOLDER" ComponentGroupName="%(ProjectReference.Filename)_Project" SuppressCom="true" SuppressFragments="true" SuppressRegistry="true" SuppressRootDirectory="true" AutoGenerateGuids="false" GenerateGuidsNow="true" ToolPath="$(WixToolPath)" Condition="'%(ProjectReference.PackageThisProject)'=='True'" PreprocessorVariable="var.BasePath" /&gt; &lt;/Target&gt; &lt;/Project&gt; </code></pre>
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    1. POWIX 3.6 Installer - Visual Studio 2010 (HeatDirectory)
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    1. COI'm having the same issue but so far I do not see how this solves the problem. Is DefineConstants supposed to replace the original LinkerBaseInputPaths element?
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    2. CO@jpierson I've updated the answer, let me know if this doesn't answer your question.
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    3. COOk, Thanks to you I believe I have it all working now. I was missing the attribute PreprocessorVariable="var.BasePath" on your HeatDirectory element because of the formatting. Next I had to replace all of the SourceDir references in my other WIX project files with references to var.BasePath including in my XSLT transform.
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