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Code reorganization and helpers

Viktor Kuncak requested to merge github/fork/SimonGuilloud/theories-helpers into main

Created by: SimonGuilloud

Printer file moved to utilities New organisation of helpers, new helper file for RunningTheory and their elements. Can show Justifications SCProofCheckerJudgement now contain the proof they refer to, no need to pass it explicitely along anymore. Other small changes.

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