@monsky, This is an interesting question.
Jacoco gives you the flexibility to include or exclude a specific set of classes in your coverage. IF you want to find code coverage of only dependent classes, you can do 2 things.
Find out recursively all the dependent sub-modules of the class that need to be covered. Using this, when you invoke Jacoco, mention an explicit list of classes that you want to include coverage for. You can do this using the includes element of Jacoco .
In case you have a ready list of files that you want to cover, just mention it in the includes syntax, you do not have to generate a dynamic list of dependencies. I would however go with 1.
You can use intellij IDe to do it as well http://jetbrains.com/idea/webhelp/analyzing-dependencies.html