Hello,
I managed to get things working and also automated, with my currently Maven based setup, initially with the help of the ticket instructing to invoke Ant for report generation rather than depend on the straightforward assumptions of Maven plugin.
The setup of this specific project does not use agents, rather a customized classloader that introduces branch flips and other shenanigans to the bytecode on the go. This meant that there were always at least two class instances, one in the main app classloader telling the specialized classloader "please take this class and modify it", and the other in the modifying classloader.
In fact, I re-modelled the bytecode instrumentation a bit according to what JaCoCo does, to make the transformation deterministic, and only have a single additional class definition (before there were hundreds of different variations of the class during one run, all with different branch flips)
It would help to change the documentation to say that "exclude classloader names" are _class names_ of classloaders (*AppClassLoader), not the newer java classloader name ("app"). Maven docs did not have the default value hint that the plain agent instructions have.
Once I got it to ignore all other classloaders except the one I was interested in, and made the class modifications deterministic on bytecode and thus class identity level, things went smoother. I shall write at some point an explanation what it does, how it does, and how it interacts with JaCoCo (classdump, classloader exclusion etc)
Next thing to tackle is how exceptions are handled, but that will be a separate post.
Many thanks for working on a great toolkit!