[FIX] Write updated doughnut file to disk at the end of `DicomReorgWorkflow` and `BidsConversionWorkflow`

[michellewang]

• Closes #254

[codecov[bot]]

Codecov Report

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

Project coverage is 98.64%. Comparing base (3f02887) to head (373e967).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #260 +/- ## ========================================== + Coverage 98.52% 98.64% +0.11% ========================================== Files 28 28 Lines 1760 1766 +6 ========================================== + Hits 1734 1742 +8 + Misses 26 24 -2 ```

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