Create Ant task:

<clover-embed-runtime targetFile="jar/war/ear file"/>

which will put all Clover's runtime classes into targetFile.

Unzip all com_cenqua_clover.* and com.atlassian.clover.runtime.* classes from clover.jar archive which is currently on a classpath (we've got a trick how to find it - see searching for clover.license) into a temporary directory and next put them into jar (use Ant <jar/> task for this or handle zip directly).