Refactor CuBIDS to support file collections

[tsalo]

Closes .

Changes proposed in this pull request

• Add file collection entities (echo, mt, flip, part, and inv) to NON_KEY_ENTITIES.
• Replace "modality" with "datatype" when applicable.
• Draft function to resolve BIDS URIs in IntendedFor definitions (resolve_bids_uri).
• Use BIDSLayout when possible, instead of string manipulation and globbing.

Documentation that should be reviewed