D2b

- FIX: Fix bug in IntendedFor `resolve` function. Properly add IntendedFor filepaths to json sidecars in scenarios where IntendedFor is a list and the target acquisition has multiple runs. Add e2e test to cover this scenario.
- MAINTENANCE: Update black to stable version and sync dev tool versions in `.pre-commit-config.yaml` with `poetry.lock` versions

- UPDATE: Change how files are sorted. Files are first sorted by `SeriesNumber` (if JSON and field exists), then by filepath.

- FIX: Fix bug in parameters passed to the `prepare_run_parser` hook
- UPDATE: Add `prepare_collected_files` hookspec
- MAINTENANCE: Split linter CI into two separate workflows (`lint.yaml` + `superlinter.yaml`)