Add a validate subcommand for post-export sanity checks

[gaurav]

Summary

Adds pubmed2db validate <dir>, which inspects a finished JSON export (a
directory of NDJSON shards) and writes an archivable, gated
validation_report.json. It answers "does this export make sense?" after an HPC
run. Targets initial-implementation so it can be reviewed after the base branch.

Four checks, split into an offline phase (fast, deterministic) and an
online phase (Entrez eutils cross-checks; skip with --offline):

1. structure — every line parses as JSON and matches the exporter's exact
   10-field record shape (reuses export._document/month_to_abbrev); flags
   malformed lines, missing/extra fields, nulls, bad ids, invalid months, and
   cross-shard duplicate PMIDs. Per-shard reservoir sampling keeps memory bounded.
2. coverage — exported count vs. two denominators: the live Entrez total
   (einfo, a loose sanity band) and the local latest_article count (a
   shortfall is an error — rows were dropped); plus drift vs. --previous-report.
3. field_validation — a seeded sample re-fetched via batched efetch and
   compared field-by-field (fuzzy abstract via difflib). Journal name/abbrev
   are warning-only (different source); a sampled PMID PubMed no longer serves is
   an error.
4. deletions — samples DB deleted_pmids not reinstated by a later version,
   confirms they're absent from the export and gone from PubMed.

Report & gating

The report leads with errors/warnings arrays that are empty on a clean
run; the stdout summary is quiet on success and loud on findings. Exit is
non-zero on errors (--fail-on-warn extends to warnings) so it can gate a
pipeline. The DuckDB database and a previous report are optional inputs used
when present and left blank (noted in skipped_checks) when not.

Notes for review

• All network funnels through one validate._eutils seam (rate-limited,
  retrying), which tests monkeypatch — the suite stays fully offline.
• Deletion detection sources from the DB only; previous-report-based drop
  diffing is deferred (would need a PMID manifest sidecar) — see FUTURE.md.
• No new dependencies (requests, lxml already present).

Testing

• uv run pytest — 51 passing (34 existing + 17 new), no network.
• Manually verified CLI output on a clean export (PASS, exit 0) and a broken
  export (FAIL with itemized errors, exit 1).

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