Jean-Noel, thanks for the feedback but its reads as a mixed message. I'm not sure if this is fixed or there is more work to be done.
I suspect more work.
When you say it better respects the dependency tree, are you saying that the output is not correct?
Looking at the 2.9 output, I'm suspicious about why the JRE_CONTAINER is third on the classpath (i.e. splattered in amongst everything else).
Also why is M2_REPO/javax/persistence/persistence-api/1.0/persistence-api-1.0.jar second?
Its a transitive dependency of org.hibernate:hibernate-annotations:jar:3.2.1.ga:compile.
The ordering doesn't look like the order I expect.
Would you be able to re-arrange the 2.9.classpath into the order you expect?
I've pulled out the dependency mojo which uses a shared component for building the tree.
I vaguely recall something about that not being 100% correct but I think I'll look at switching the m-e-p implementation from a home-grown to shared components.
At least that will mean it can get fixed once.
Work is busy at the moment so progress may stall for a bit.