Thanks for joining me in conversation on this, I find it very interesting to find this stuff out, However what i meant in that last paragraph was this. I have a recompiled binary package with lots of functions and the linkmap. I write a 'plugin' for said application, i wish to extend the main() function, so by extending it, im in effect adding to that function. it would be no difference to decompiling the binary and adding the cod inline. Or does java not work like this> I had a flick through the JavaAPIdoc it seems that it uses a simple stack management system so any bukkit plugins should be extending the main execution stack.
