fix: harden MCP, native HNSW gates, and ruvector 0.2.37

[ruvnet]

Summary

• fixes ruvector mcp start and keeps MCP stdout JSON-RPC-only (closes mcp start: console.log in ONNX loader corrupts stdout JSON-RPC → 'Failed to connect' in Claude Code #710, closes mcp start: server registers handlers but never listens — mcp-server.js gates bootstrap on require.main === module, which cli.js can never satisfy #715)
• replaces raw-shell worker execution with argument-vector process execution
• restores the JavaScript wrapper default to native HNSW instead of accidental FlatIndex
• makes functional, learning, performance, and recall CI require the native backend
• repairs the aggregate npm CI job and the pre-existing workspace rustfmt failure
• removes the workspace critical tar advisory, updates Google Redis/protobuf resolution, and prepares ruvector@0.2.37
• corrects the Shor milestone table and distinguishes the Schnorr/QAOA hybrid result (closes The "State of Play" factoring table appears to contain misleading / incorrect entries #712)
• adds the repository-wide SOTA, security, and package review

Root causes

The CLI loaded the MCP server as a module whose guarded main() was never invoked. ONNX diagnostics also wrote to stdout and could corrupt the stdio transport. Separately, the JavaScript wrapper forwarded an omitted hnswConfig as undefined; N-API mapped that to None, selecting FlatIndex instead of the Rust core HNSW default. CI omitted optional dependencies, so its performance and recall jobs exercised the fallback rather than the native engine.

Validation

• cargo check --workspace --all-targets --locked — passes across the workspace
• cargo fmt --all -- --check — passes
• cargo audit and cargo deny check advisories — pass
• native npm test — passes 73 CLI checks plus database, MCP handshake/stdout, signals, access policy, and startup guards
• release workflow scripts locally reproduce 3.30x HNSW speedup and 0.95 recall (gates: 2x and 0.88)
• npm run build && npm run verify-dist — passes
• npm pack --dry-run --json --ignore-scripts — valid 0.2.37 tarball, 153 files
• publishable-package audit — no high or critical advisories
• workspace audit — no critical advisories; 12 high and 12 moderate transitive findings remain for breaking-upgrade follow-up

Supply-chain note

GitHub does not currently expose this repository dependency graph to dependency-review-action. That single service-dependent step is soft-failed while #689 tracks the prerequisite; Cargo audit, Cargo deny, npm critical audit, and lockfile integrity remain hard gates.