Hi Denis,
Thanks for investigating on this; and even more, for sharing conclusions. It is a pity I could not detect this side-effect by myself. It's also a pity I get this feedback so late, I thought introducing such a regression would have been the cause of immediate complaints. IMHO, it shows Jenkins is under-used by most people.

About coverage, it's up to people who consume these coverage reports to decide what they need/want. I am afraid all this coverage things are currently not used at all, so no-one would care in case we remove Emma or Jacoco.

Currently, we still have to use Emma if we want coverage since we don't have a way to get "continuous" reports easily with Jacoco (BTW Max made some tentative usage of Sonar, and Jonathan Fuerth submitted a GSoC subject for a Jacoco plugin in Jenkins).
Then I think the wiser and simpler solution would be to disable Jacoco.

We can think of Jacoco as a progress since it allows developers to consume reports directly in their IDE (see a 3-weeks older mail of mine for more details). But, once again, nobody use it, so we can ignore it.

In a mid to long term view, we will get rid of Emma to use only Jacoco.
Currently, we are stuck to Emma and then it seems like we need to disable Jacoco. I do that immediatly in parent.

Regards,
--
Mickael Istria
Eclipse developer at JBoss, by Red Hat
My blog - My Tweets