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3.2 M4 This is maybe related to bug 123224 Attaching thread dump...
Created attachment 34911 [details] thread dump
Not a dup of 123224. The problem is that the update job could initialize the Java model hence requesting a Java model lock. So the update job must specify a scheduling rule. The deadlock occurs since the PDE feature builder builds a project resulting in a delta notification which marks the type history as inconsistent.
Fixed.
Verified using I20060328-0010