You want, break out once, expand a lot. Then you will want to use HTML5 for this. You can use Apache Cordova directly, but you want to use a service like Telerik AppBuilder, Adobe Phonegap or Intel XDK.
As for your question, it is best to use a good method of obfuscating JavaScript source code to protect your sources before publishing. There is no such thing as a 100% complete proof of solution when it comes to JavaScript obfuscation, but professional tools like JScrambler can go a long way. At least JScrambler, I know that it supports Mobile and HTML5, which is good, because they guarantee that the resulting code is compatible.
There are other tools, even free ones. But be careful, there are many other tools that do obfuscation, coding / packaging, or minfication, which seem to provide protection, but are reversed within minutes. So, if you really do not know how to tell the difference, I recommend you rely on a professional service.
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