Refactor to support multiple BIDS datasets and improve workflow selection

### Summary
Currently, the pipeline uses a `samples.tsv` file structured for a single BIDS dataset. To scale up and support multiple BIDS datasets more flexibly:
- **Samples file refactor:**
- Add columns such as `output_bids_dataset` to enable output paths for multiple BIDS datasets within the same table.
- **Workflow selection:**
- Current method selects the workflow by searching for a substring in the `acq` field; this is potentially fragile and unintuitive.
- Proposal: introduce an explicit column that defines either the type of input data or the specific workflow to use per sample, making selection clearer and more robust.

### Suggestions
- Redesign the `samples.tsv` schema to enable scalable, multi-dataset processing.
- Add an explicit column for workflow selection to reduce hackiness and improve maintainability.
- Consider this an opportunity to incorporate breaking changes to the file and workflow logic.

### Breaking Changes
- This update will likely introduce breaking changes both to file formats and workflow logic. Document migration and update notes accordingly.

### Benefits
- Future scalability for projects with multiple BIDS datasets.
- More maintainable, explicit workflow selection process.
- Reduced risk of errors from implicit/inferred logic.

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Feedback on the proposed schema or naming conventions would be appreciated before implementation.