WiX: Digitally Sign BootStrapper project

by 
  <Target Name="UsesFrameworkSdk">
    <GetFrameworkSdkPath>
      <Output TaskParameter="Path" PropertyName="FrameworkSdkPath" />
    </GetFrameworkSdkPath>
    <PropertyGroup>
      <Win8SDK>$(registry:HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SDKs\Windows\v8.0@InstallationFolder)</Win8SDK>
    </PropertyGroup>    
  </Target>

  <Target Name="UsesSignTool" DependsOnTargets="UsesFrameworkSdk">
    <PropertyGroup>
      <SignToolPath Condition="('@(SignToolPath)'=='') and Exists('$(FrameworkSdkPath)bin\signtool.exe')">$(FrameworkSdkPath)bin\signtool.exe</SignToolPath>
      <SignToolPath Condition="('@(SignToolPath)'=='') and Exists('$(Win8SDK)\bin\x86\signtool.exe')">$(Win8SDK)\bin\x86\signtool.exe</SignToolPath>
    </PropertyGroup>
  </Target>

  <Target Name="SignBundleEngine" DependsOnTargets="UsesSignTool">
    <Exec Command="&quot;$(SignToolPath)&quot; sign /d &quot;App Setup&quot; /t http://timestamp.digicert.com /a &quot;@(SignBundleEngine)&quot;" />
  </Target>

  <Target Name="SignBundle" DependsOnTargets="UsesSignTool">
    <Exec Command="&quot;$(SignToolPath)&quot; sign /d &quot;App Setup&quot; /t http://timestamp.digicert.com /a &quot;@(SignBundle)&quot;" />
  </Target>

This works well for me. Either you do it during the build, or you need to use insignia.
Ex:
http://wixtoolset.org/documentation/manual/v3/overview/insignia.html

insignia -ib bundle.exe -o engine.exe
... sign engine.exe
insignia -ab engine.exe bundle.exe -o bundle.exe
... sign bundle.exe

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