added a comment - - edited
As Evgeny Mandrikov mentionned, Jacoco made the trick for me & is plugin agnostic.
I have use it on a real entreprise & multi-module maven projects :
Each of them have unit tests and C-web have integration test when the war is deployed.
Those integration-test are composed of Jwebunit and SoapUi.
For each module let say we have a 10% coverage.
But obviously C is using indirectly A & B so it will be nice to report the coverage done during the integration-test to the respective modules (A & B)
The trick is to not seperate unit & integration test and generate the jacoco.exec in one place.
Each module will append his result to the same file as long as the tests are run sequentially.
So the sonar maven plugin will analyse 3 times the same file for each modules.
And after, the coverage results could be A(30%), B(30%) and C (10% unchange of course)
Of course if you are really interested to seperate IT report coverage and Unit report coverage, use the same trick with two files for each need.
The difficult part is to agregate report file with tcp stuff, produced in a distant J2ee server ;(.
For this purpose of merge, there is a ant task to merge files.