Update examples to remove obsolete variables

[clmould]

Description

Closes #3950
Update the example/data files to remove obsolete variables. Removed the scan_MFILE.DAT and the plot_scan from examples.ipynb as that function is used in scan.ipynb.

Checklist

I confirm that I have completed the following checks:

• My changes follow the PROCESS style guide
• I have justified any large differences in the regression tests caused by this pull request in the comments.
• I have added new tests where appropriate for the changes I have made.
• If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
• If I have made documentation changes, I have checked they render correctly.
• I have added documentation for my change, if appropriate.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 46.09%. Comparing base (b0a0128) to head (107272c).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3978   +/-   ##
=======================================
  Coverage   46.09%   46.09%           
=======================================
  Files         123      123           
  Lines       28888    28888           
=======================================
  Hits        13316    13316           
  Misses      15572    15572           

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