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Spyros,We've been using Prism & it's been working great but unfortunately it's not available anymore in FF 4.We've moved to Chrome which also has a similar lock down feature (application shortcut) that you can lock down further with a chrome js extension.A way to minimize these problems is to use a single page application from where BTFs are called in dynamic regions.But this too can be limited if you have lots of apps or use an sso page or some other portal entry point page..And apart from these browsers lock down trick, today there is no clean design patterns to avoid these problems.
Jean-Marc,Thanx for the feedback! As you can see the post is old (probably FF4 was not around then :) ).Unfortunately it seems there is no way to avoid them. Let's hope in the future will be some :)