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Update of documentation for research and some tweaks to the paths

Mariana Isabel Vivas Albornoz requested to merge update_documentation into master

In this merge request I am:

  • Adding hadronic calibration documentation (first version at least)
  • Fixing the SM documentation
  • Added subsections to the paths for better navigability
  • Added a containers tutorial under tutorials for research
  • Changed Jupyter notebooks -> physlite tutorial, under tutorials for research

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