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TobyFruthParson
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These are my go-to links for ThinApp and Java:

http://blogs.vmware.com/thinapp/2008/10/step-by-step-in.html

http://blogs.vmware.com/thinapp/2011/03/the-power-of-applink.html

http://blogs.vmware.com/thinapp/2010/01/step-by-step-instructions-on-how-to-thinapp-newer-java-versi...

http://blogs.vmware.com/thinapp/2010/06/java-16-tweaks.html

I know you want to avoid using AppLink if you can, but maybe it's worth considering that your Java package can be both an independent JRE application as well as an Optional or RequiredAppLink for other applications.

Toby Fruth, Sr. Specialist, The Parsons Corporation