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Fixes #2846. One of the challenges of the Java bindings is that the garbage collector can delete unused objects at any time in any order. This is an issue with CVC4's API because we require all `Expr`s to be deleted before the corresponding `ExprManager`. In the past, we were using `NewGlobalRef`/`DeleteGlobalRef` on the wrapper object of `ExprManager`. The problem is that we can have multiple instances of the wrapper that internally all refer to the same `ExprManager`. This commit implements a different approach where the Java wrappers hold an explicit reference to the `ExprManager`. The commit also removes some unused or unimportant API bits from the bindings.