I thought this would be useful to document but I don't have the time to blog it. If you're looking to update the client dependency framework, presumably using CI such as Jenkins or TeamCity then you can do the following:

<Project>
<!--The rest of the xml-->
  <Target Name="UpdateClientDependencyFrameworkVersion" AfterTargets="CopyAllFilesToSingleFolderForMsdeploy">
    <PropertyGroup>
      <VersionXPath>/clientDependency/@version</VersionXPath>
      <!-- You can test by setting a value here -->
      <!--<CdfVersion>2</CdfVersion>-->
    </PropertyGroup>
    <ItemGroup>
      <CdfConfigFiles Include="Config\ClientDependency.config" />
    </ItemGroup>
    <Message Text="Updating client dependency framework to version $(CdfVersion)" Importance="high" />
    <XmlPoke  XmlInputPath="@(CdfConfigFiles ->'$(WPPAllFilesInSingleFolder)\%(RelativeDir)%(Filename)%(Extension)')"
            Query="$(VersionXPath)"
            Value="$(CdfVersion)"/>
  </Target>
</Project>

This build task will insert in to /Config/ClientDependency.config a new version, which equals the same as the custom build property CdfVersion.

Using your CI server you'll need to provide that value. In TeamCity you can use %build.counter%, and I'm sure a similar number exists in other systems.

Also FYI: For config transforms of everything in the config folder checkout this topic.