feat: write references.json into each package; address review

When packaging an entry, write a references.json alongside entry.json listing
the Benchling objects the entry points at (entities, classified links, results
tables), discovered from the entry's note links and fields. No records are
fetched -- discovery only.

- entry_references.summarize_references(entry): JSON-serializable payload
  ({schema_version, entities, links, results_tables}); REFERENCES_SCHEMA_VERSION.
- entry_packager._create_metadata_files: emit references.json + document it in
  the package README.

Review fixes (Greptile + Copilot):
- Drop empty-string entity IDs in _field_value_ids, matching the note-link guard.
- Narrow RESULTS_TABLE_NOTE_TYPES to {"results_table"} -- the only type carrying
  assayResultSchemaId; avoids latently capturing generic/registration tables.
- Modernize typing (dict/list/tuple) on the 3.11+ codebase.
- Remove committed spec/entry-link-types.json (relocated to the project's
  scripts/ as a research artifact) and its drift-guard test.

Full suite green (437).

Refs #143 #389 #68

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: drernie