EclEmma is based on JaCoCo and starts JVM with JaCoCo agent in "tcpclient" output mode (see
http://www.jacoco.org/jacoco/trunk/doc/agent.html) that connects back to EclEmma to report code coverage. Subprocesses obviously do not have agent magically. Tracking of subprocesses is tough OS-dependent task with many corner cases, even not counting the need to modify startup arguments. This statement is based on 3 years of experience in development/maintainance of process-tracking application that is part of a bigger commercial product. So I'm pretty sure that we'll never add to JaCoCo (and hence EclEmma) ability to automatically attach agent to subproesses. However if you control the creation of subprocess, then you can modify it so to use agent. But EclEmma accepts only one connection. Not sure about added-value if we allow multiple connections, because this raises quite some questions and there are simpler alternatives:
there is no problem with number of connections in case of usage of JaCoCo outside/without Eclipse and EclEmma, which is actually the way to integrate gathering of code coverage into automated build process;
or child processes can save coverage data into file (JaCoCo agent output mode "file" that is default) that can be imported into Eclipse using EclEmma.
Regards,
Evgeny