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See forum post: http://www.eclipse.org/forums/index.php/r/reply_to/709817/ Tomcat overwrites the TCCL set by synthetic context on request.
Also application specific trace is similarly affected. A web app inside a scope ends up with a separate application trace directory to that of the scope. We should probably document both these effects together.
The correct link to the forum: http://www.eclipse.org/forums/index.php/t/229437/
Fixed in documentation commit 084fe3a10755dde1efc6118986b849dd9be0fb35.