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I’m interested in an executed script allowing user input to modify the process and corresponding source.
What precedents exist to implement such a structure?
Yes, depending on what is meant.
Consider such projects as ObjectWeb ASM (see the the ASM 2.0 tutorial for a general rundown).
Trying to emit the-would-need-to-be-decompiled Java source code is another story: if this was the goal then perhaps the source should be edited, re-compiled, and somehow loaded in/over. (This is possible as well, consider tools like JRebel.)
Happy coding.