Generalize entities [Phase 2]

[kaitj]

Background

PR #86 attempted to replace hardcoded sub-/ses- entity assumptions with schema-driven discovery. It was never merged because of conflicting changes introduced by other PRs. The codebase also added in a BIDSSchemaAdapter, along with associated functions since #86 was originally opened. There was also PR feedback to be tackled alongside trying to resolve the conflicting changes.

These phased issues are intended to introduce stacked PRs that supersede #86

Goal

Add new CLI options and deprecation warnings without changing indexing behavior. Extend index schema with columns for dataset metadata.

Scope

• CLI: Add --filter and --schema flags
• Deprecation warnings for --subjects and include_subjects
• Index schema: Add dataset_name, dataset_type, bids_version columns
• Filter matching logic (internal _match_filters)