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Hello,
First, there's no shame to use an encoder ...
Secondly, I can talk of my personal experience with Zend Guard.
You can just encode your module and not Xoops.
You can also exclude some files (from your module) to encode.
But you will need the Zend Optimizer to be installed on the server and depending of its version, the level of encryption will be different.
Bye,
Hervé