Align public-repo metadata/docs with verifiable sample artifacts and v2.4.0 schema semantics

[Copilot]

This PR resolves cross-file inconsistencies across documentation and manifest metadata by reconciling claims against artifacts that actually exist in the public repository. It standardizes versioning, schema semantics, sample/file integrity data, and quickstart references into a single internally consistent source of truth.

• Scope + source-of-truth normalization

  • Reworked MANIFEST_v2.json to explicitly cover the public sample repo scope (not commercial full-release binaries).
  • Replaced non-verifiable full-package entries with verifiable sample artifacts (ethno_sample_400.*, quickstart.ipynb) and updated SHA-256/byte-size metadata.

• Schema/version consistency across docs

  • Synchronized README.md, METHODOLOGY.md, UPDATE_POLICY.md, llms.txt, and quickstart.ipynb on:
    • current version (v2.4.0)
    • 16-column schema representation
    • field semantics for partner_cid, inchi_key, iupac_verified, partner_match_method
  • Removed/rewrote contradictory statements (e.g., stale version references, non-existent manifest sections, mismatched field counts).

• Sample-vs-doc alignment

  • Updated README front matter and tables to reflect actual sample shape/types/null behavior from ethno_sample_400.json / .parquet.
  • Clarified logical-vs-serialization behavior where needed (notably inchi_key in sample parquet being currently all-null).

• Quickstart/documentation corrections

  • Updated notebook examples/citation text to match current schema (16-column) and valid split usage (train).
  • Updated noise exclusion header context to match current release lineage while preserving audited historical notes.

{
  "manifest_scope": "public_repository_sample",
  "files": {
    "json_sample": {
      "filename": "ethno_sample_400.json",
      "size_bytes": 226228
    },
    "parquet_sample": {
      "filename": "ethno_sample_400.parquet",
      "size_bytes": 33485
    }
  }
}