If you want to limit your HTML report to contain classes which have been modified since a previous build (using information from a VCS such as git or hg), then you'd have to build such query on your own and next pass list of files to the <clover-report> task (see <fileset> + <testsources> options).
See also: https://answers.atlassian.com/questions/86543 question.
If you would like to perform a logical or arithmetical operation (such as XOR or subtraction) on coverage data from two different builds, then unfortunately such feature is not available right now. A feature request is reported here https://jira.atlassian.com/browse/CLOV-1024.
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