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Misc fixes

Laurent Petre requested to merge misc-fixes into main

This MR fixes two known bugs:

  1. The determination of the MergeCSV.py output path, which was always resolving to an absolute path
  2. The application of the DAQ masking, which was no longer applied at all after making it a configurable flag

See commits messages and content for more details.

Edited by Laurent Petre

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