Revert "Revert "Deprecate methods in JavaPluginLoader and PluginClassLoader""

This reverts commit 2986abda0cd54ab5b5675eb6b6ed861db8f3de42.

Conflicts:
	src/main/java/org/bukkit/plugin/java/JavaPluginLoader.java
Move the plugin loader back to Libkit.
This also adds in some ASM fixes from Surge.