Make --recon-spec a required argument

[tsalo]

Closes #374.

Changes proposed in this pull request

• Make --recon-spec required.
• Fix outdated help string for --recon-spec (we use YAMLs instead of JSONs now).
• Note in --config-file's help string that it is currently not used.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 50.44%. Comparing base (06cfe29) to head (713c332).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #375   +/-   ##
=======================================
  Coverage   50.44%   50.44%           
=======================================
  Files          55       55           
  Lines        8139     8139           
  Branches      944      944           
=======================================
  Hits         4106     4106           
  Misses       3794     3794           
  Partials      239      239           

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