Reconcile PlonK and PlonkUp paper with the implementation

[moCello]

Describe what kind of specification you want to have created

• Add comments to the code-base:
  • make sure that every step of the protocol can be found in the code implementation when searched
  • mark the sections where the implementation differs from the paper and explain why and how they are different

[moCello]

Closing this issue because it has been broken into the following smaller issues to better keep track of the progress being made:
Setup: #633
Proof: #643, #644, #645, #646, #647, #648
Verification: #639, #640, #641, #642

Edit:
Reopening because braking up showed not to be feasible.