Cleaned up CMT lib by refactoring away a couple common functions

[jarry-xiao]

• Created a function called traverse_to_parent to abstract away the ugly (and highly duplicated) code that hashes a reference node up the tree
• Created a function inside the ChangeLog class that handles proof node or leaf replacement. If this existed months ago, we would have never introduced the bug in replacing the RML
• Use empty_node_cached when possible (O(N^2) -> O(N)) preprocessing
• Refactored append to be more easily readable
• Moved most direct assignment of variables into functions

All test cases pass and smoke test is chugging along

[jarry-xiao]

This PR would be better if we could refactor the remaining bit math to normal modular arithmetic.

Also, what does Moved most direct assignment of variables into functions mean?

Modular arithmetic will not save you when you do a wrapping sub for your index (unless we want to change those to i64s)