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AJDT doesn't include the outjar jar in the classpath for run targets on a project. Trying to run a main class pops up an empty dialog for me. JUnit chokes on running. Work around: manually add the output jar to the run classpath.
Sian - assigning this to you since you did the work for the run targets.
Fixed in 1.2.1 yesterday. 1.3 fix to come..
Fixed in 1.3 in the latest build