Merged input yaml records seed used

[lrobion]

Closes #120.
The merged-input.yaml generated in the output directory now records the seed that was used for a simulation even if Forced Seed was set to false in the original input.
Re-running a simulation with merged-input.yaml now reproduces (bitwise) the results of the original simulation. It is now an exact reproducibility artefact rather than an exact record of the user inputs (same logic as resolving the relative paths in inputs files to absolute paths before recording them).

E.g:
With this in the input.yaml passed to APCEMM:

  RANDOM NUMBER GENERATION SUBMENU:
    Force seed value (T/F): F
    Seed value (positive int): 0

The merged-input.yaml will be:

  RANDOM NUMBER GENERATION SUBMENU:
    Force seed value (T/F): T
    Seed value (positive int): =Actual value of the seed used by the simulation=