build-release.xml

<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
  <PropertyGroup>
		<ScriptsDir>Layouts\MyCoolProject\Scripts</ScriptsDir>
		<ManifestPath>pkg\Release\MyCoolProject</ManifestPath>
	</PropertyGroup>
	<ItemGroup>
		<ExcludedFiles Include="
			$(ScriptsDir)\jquery-1.9.1.js;
			$(ScriptsDir)\backbone.js;
			$(ScriptsDir)\backbone-sharepoint.extensions.js;
			$(ScriptsDir)\backbone-sharepoint.odata.js;
			$(ScriptsDir)\backbone-sharepoint.soap.js;
			$(ScriptsDir)\backbone-super.js;
			$(ScriptsDir)\underscore.js"
		/>
	</ItemGroup>
	<UsingTask TaskName="FindInEnumeration" TaskFactory="CodeTaskFactory"
			   AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.v4.0.dll">
		<ParameterGroup>
			<SourceFiles ParameterType="Microsoft.Build.Framework.ITaskItem[]" Required="true" />
			<Files ParameterType="Microsoft.Build.Framework.ITaskItem[]" Required="true" />
			<Result ParameterType="Microsoft.Build.Framework.ITaskItem[]" Output="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 filesToFind = Files.Select(item => item.GetMetadata("FullPath")).ToArray();

					Result = SourceFiles
						.Where(file => filesToFind.Contains(file.ItemSpec))
						.ToArray();
						
					return true;
				}
				catch (Exception ex)
				{
					Log.LogErrorFromException(ex);
					return false;
				}
				]]>
			</Code>
		</Task>
	</UsingTask>

	<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>

	<!-- It's possible to override some targets defined in 
		c:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v11.0\SharePointTools\Microsoft.VisualStudio.SharePoint.targets
		that allow to insert custom actions during publishing of SharePoint project
		-->
	<Target Name="BeforeLayout" Condition="'$(Configuration)'=='Release'">
		<FindInEnumeration Files="@(ExcludedFiles)" SourceFiles="@(EnumeratedFiles)">
			<Output ItemName="Result" TaskParameter="Result" />
		</FindInEnumeration>
		<ItemGroup>
			<!-- EnumeratedFiles defined in Microsoft.VisualStudio.SharePoint.targets
				and contains ALL project files, so we need to remove excluded files
				from this enumeration. After that they will NOT be copied over to destination WSP
			-->
			<EnumeratedFiles Remove="@(Result)"/>
		</ItemGroup>
	</Target>

	<Target Name="AfterLayout" Condition="'$(Configuration)'=='Release'">
		<!-- We have to exclude files from manifest.xml separately -->
		<ExcludeFromManifest Files="@(ExcludedFiles)" ManifestPath="$(ManifestPath)" />
	</Target>

</Project>