ExcludeFromManifest.xml

<UsingTask TaskName="ExcludeFromManifest" TaskFactory="CodeTaskFactory"
  		   AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.v4.0.dll">
		<ParameterGroup>
			<ManifestPath ParameterType="System.String" Required="true" />
			<Files ParameterType="Microsoft.Build.Framework.ITaskItem[]" Required="true" />
		</ParameterGroup>
		<Task>
			<Reference Include="System" />
			<Reference Include="System.Core" />
			<Reference Include="System.Xml" />
			<Reference Include="System.Xml.Linq" />
			<Reference Include="Microsoft.CSharp" />
			<Using Namespace="System" />
			<Using Namespace="System.Reflection" />
			<Using Namespace="System.IO" />
			<Using Namespace="System.Linq" />
			<Using Namespace="System.Xml.Linq" />
			<Using Namespace="System.Net" />
			<Using Namespace="Microsoft.Build.Framework" />
			<Using Namespace="Microsoft.Build.Utilities" />

			<Code Type="Fragment" Language="cs">
				<![CDATA[
				try
				{
					var excludedFiles = Files.Select(item => item.ItemSpec).ToArray();

					var manifestPath = ManifestPath.TrimEnd(new[] { '\\' }) + @"\manifest.xml";
					var manifestXml = File.ReadAllText(manifestPath);
					var manifest = XElement.Parse(manifestXml);
					var excludedElements =
					manifest.Descendants().Where(element => element.Name.LocalName == "TemplateFile")
						.Where(element => excludedFiles.Contains((string) element.Attribute("Location")));

					excludedElements.Remove();
					manifest.Save(manifestPath);
					return true;
				}
				catch (Exception ex)
				{
					Log.LogErrorFromException(ex);
					return false;
				}
				]]>
			</Code>
		</Task>
</UsingTask>