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I created a profile, and then removed an IU from that profile. Looking at the operands, the default Bundle fragment (CU) is not attached. This means that while the IU is removed, it's not unconfigured. See DirectorApplicationTest#testEPPProfileRemoveIU for the test case.
This appears only to be a problem with certain IUs. In this case, ch.logback.* was installed in the profile, but these IUs are not really needed, that is, on the next operation the planner wants to remove them. We first slice the profile, and attach the fragments to only those things in the slice. These IUs are not in that slice (hence they don't have the default CU).
This is actually not a problem with p2, but rather a problem with the profile we started from. That is, p2 created a bad profile (see bug 323322), and now when use this, things go south pretty quickly. (Garbage in -- Garbage out).