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In version 1.4.0.20060307084510 of AJDT along with Eclipse 3.2M5a, the "AspectJ Tools" menu is not displayed in the pop-up context menu associated with Java projects in the Package Explorer.
Just as a note, there's been a mailing list thread about this: http://www.eclipse.org/newsportal/article.php?id=1560&group=eclipse.technology.ajdt#1560 with the conclusion that this is probably due to bug 130571.
Closing, as WTP bug is fixed.