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I'm also wondering how to securely protect the HTML and JS source files that will resides in the program files when installed.
Looking at some of the featured applications developed in HTML & AJAX, it seems that nobody had been able to protect those.
It don't believe there is a way to currently do this, an obvious benefit to doing developement with Flex and/or Flash, but according to some people on this forum, those files can be cracked (probably not by the average person though). It would be nice to have some type of encrypted container or DRM added to the published files.
Is there any updates to this? This thread is over a year old, but I am just starting out with AIR and was wondering how to protect my html and js files from being viewed/modified as well.