The error message:

jar:file:/Users/pkamal/clover.jar!/clover.xml:76: com.cenqua.clover.registry.NoSuchRegistryException: Clover registry file "/Users/pkamal/development/src/trunk/.clover/clover2_4_2.db" does not exist, cannot be read or is a directory

Does not make it clear to the user that their code has not been instrumented, hence their clover.db has not been created.
We should add this to the error message, including a suggestion to run "clean" first before retrying.