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If you have a project with multiple src folders and in the active build configuration, one of those source folders is excluded (as in the case of org.aspectj.ajdt.core). If you create another src folder then all src folders are included in the active build configuration.
Forgot to say that this is with Eclipse 3.1 and AJDT build: 1.2.1.20050630163114 - I haven't tried it on Eclipse 3.0.
Confirmed on Eclipse 3.0
Fixed