The Java environment in which Java class files are executed is a subsystem with its own policies. C/C++ on the other hand being a legacy language is likely to have its own set of policies.
What I am trying to say is when you use JNI on a mammoth scale, you are going to have problems. You lose your write once run anywhere advantage of java as your C code may produce unexpected problems on another machine. It may also be slow because your code is entering a whole new different environment, security policies may throw an error anytime and there lots more areas where errors can occur.
I said this in part 1 and I say it again: use JNI only when you really need to.
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