Add Semantic Scholar article enrichment, citation graph, and recommendations

[imaurer]

Summary

• Adds optional Semantic Scholar integration gated on S2_API_KEY environment variable
• When key is present, get article output includes a Semantic Scholar section with TLDR, influential citation count, reference count, and open-access PDF metadata
• Three new article subcommands: citations, references, and recommendations — all require S2_API_KEY and exit with a clear error when absent
• Multi-seed recommendations supported: article recommendations <id1> <id2> --negative <id3>
• Rate limiting at 1 req/sec with batch lookup (up to 500 IDs) for bulk cross-referencing
• Graceful degradation: get article works fully without the key; S2 section is simply omitted
• Docs updated: docs/reference/data-sources.md, docs/getting-started/api-keys.md, and RUN.md explain the optional key and what it unlocks
• scripts/contract-smoke.sh probes S2 when key is present; skips cleanly when absent

Changes

New source client: src/sources/semantic_scholar.rs — typed API client for citations, references, recommendations, and paper detail endpoints with 1 req/sec rate limit.

Article enrichment: src/entities/article.rs — get article enriches the result with a semantic_scholar block when S2_API_KEY is set; silently skips otherwise.

New CLI commands: src/cli/mod.rs — article citations, article references, article recommendations as explicit S2-only navigation commands.

Rendering: src/render/markdown.rs — citation/reference/recommendation tables with context snippets, intents, and influential flag.

Docs and smoke: RUN.md, docs/reference/data-sources.md, docs/getting-started/api-keys.md, scripts/contract-smoke.sh, and spec coverage for all new S2 paths.

Behavior without S2_API_KEY

$ biomcp get article 22663011          # works, no S2 section
$ biomcp article citations 22663011    # exits 1: "API key required: set S2_API_KEY"

Test plan

• make check (clippy + fmt) passes
• cargo test — 647 unit tests pass
• make test-contracts — contract tests pass
• spec/06-article.md spec — 16/16 pass including new S2 tests
• Manual: get article <pmid> tldr shows Semantic Scholar section with key present
• Manual: article citations <pmid> --limit 3 returns citation table with contexts
• Manual: article references <pmid> --limit 3 returns reference table
• Manual: article recommendations <pmid> --limit 3 returns recommendations
• Manual: all three S2 commands exit 1 cleanly without key