[ENH] Rename tabular file columns to `visit_id` and `session_id`

[michellewang]

Closes #245, closes #242, closes #241.

Summary:

• New column names in manifest, doughnut, dicom directory map
  • Specifically: session -> session_id and visit -> visit_id, where session_id does not have the BIDS prefix (breaking change)
  • Sample manifest with new columns:
• Global config fields also updated accordingly SESSIONS -> SESSION_IDS, VISITS -> VISIT_IDS
• CLI arguments updated too
• Big variable renaming participant -> participant_id, session -> session_id, visit -> visit_id
  • I might have missed some instances but I think I got most of them
• Doughnut columns renaming to be more explicit about where we expect the data to be:
  • downloaded -> in_raw_imaging
  • organized -> in_sourcedata
  • bidsified -> in_bids
• Renaming of scratch/raw_dicom -> scratch/raw_imaging as previously discussed

Should be merged before #243 which I will update to reflect the changes here

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 98.52%. Comparing base (00c104f) to head (431dde1).

:exclamation: Current head 431dde1 differs from pull request most recent head de34863

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #263 +/- ## ========================================== - Coverage 98.53% 98.52% -0.02% ========================================== Files 28 28 Lines 1775 1759 -16 ========================================== - Hits 1749 1733 -16 Misses 26 26 ```

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