Handle Reform Pt. 2

This is a continuation of #331 and begins the removal of handles from the internals of the kernel. I will continue this work on all other parts of the kernel, and after we're done with this hopefully handle closing can finally be implemented.
For now, yes. `Object::handle` and `GetObjectHandle()` are inherently broken, but there's no way to take them out without first removing Handle from the rest of the codebase (like this PR does for Thread.)