feat(q2): AI-Native Synthesis MVP — discovery sections from commits + statics

[masonwyatt23]

Summary

Implements the Q2 supporting pillar from wad-d-instrumentation-genome-2-sequencing.md — a background LLM pass that converts recent commit sections + relevant static genome sections into AI-synthesized discoveries.

• New discovery section type (manifest v2 extension, additive): kind: \"discovery\" + sourceTrust: \"synthesis\" (new union value), stored at .ashlrcode/genome/discoveries/<id>.json, capped at DISCOVERY_RETENTION_LIMIT=30 (mirrors commit retention).
• scripts/genome-synthesizer.ts — CLI-only background pass that uses the existing servers/_llm-providers/ infrastructure via selectProvider().
• Wired into ashlr__grep: when discovery sections exist and keywords match, they're prepended under a ## Discoveries block ahead of commits and static sections. Static/commit ordering unchanged when no discoveries exist.

Tier gating (hardcoded at the top of synthesize())

Tier	Behavior
free	Hard-gated OFF. synthesize() returns { skipped: true, reason: \"free-tier\" } before ever touching the LLM. Even --force cannot override this.
pro	Throttled to once per 7 days per repo via .ashlrcode/genome/_synthesis-state.json.
team	Throttled to once per 24 hours per repo.
--force	Bypasses throttle for manual runs (does NOT bypass the free-tier gate).
--dry-run	Parse + score + prompt, but never write to disk.

Privacy

• Only commit-section summaries (user-authored commit messages) are sent to the LLM — never raw diff content.
• Paths matching secret patterns (secrets/, .env, *.pem, id_rsa*, credentials.json) are redacted from filesChanged lists and stripped from the prompt body before construction.

Sample discovery section (illustrative)

{
  \"id\": \"9f1c4ae27e8a3d12\",
  \"summary\": \"Recent activity tightens v1.31 SessionEnd hook diagnostics (hook-health surfacing + onboarding hero) and renames Grok references to grok-4.3 — the WAD-D telemetry path is being prepped without touching the post-commit hot path.\",
  \"evidence\": [
    { \"path\": \"hooks/session-end.ts\" },
    { \"path\": \"scripts/install-genome-hooks.ts\", \"lineRange\": [40, 120] },
    { \"path\": \"servers/_ask-router.ts\" }
  ],
  \"sourceCommits\": [
    \"1b1632a036383af3cc21a66f2cd8ac3254474eaf\",
    \"7b1430c4b44bf5984c805e71fa464721815dfb94\",
    \"d20bc62a181cc6a8135daa736ffd1e1cf31536b5\"
  ],
  \"synthesizedAt\": \"2026-05-22T22:00:00.000Z\",
  \"confidence\": 0.74
}

Files

• New: scripts/genome-synthesizer.ts, servers/_genome-discoveries.ts, __tests__/genome-synthesizer.test.ts
• Modified: servers/_manifest-v2.ts (added DiscoverySection types, \"synthesis\" to SourceTrust, \"discovery\" to kind union), servers/_genome-commits.ts (exported tokenize + renamed scoreCommit → scoreSectionMeta for reuse), servers/grep-server.ts (prepend discovery block).

Strict LLM-response validation

• Malformed entries dropped: missing summary, hallucinated SHA (not in known-commits set), wrong shape.
• Confidence clamped to [0, 1].
• Output capped at 3 discoveries per run.
• Markdown code fences (```json) stripped defensively.

Test plan

• 23 new bun:test cases in __tests__/genome-synthesizer.test.ts
• Free tier verified to NEVER invoke the mock provider (assertion in test)
• Pro tier + within 7d window → \"throttled\"
• Team tier + 36h since last run → not throttled, writes
• --force bypasses throttle
• Malformed LLM entries dropped, valid ones still write
• --dry-run writes no files, no state update, returns wouldWriteIds
• Secret-path redaction verified (no secrets/, .env paths reach the LLM)
• retrieveDiscoverySections surfaces matching discoveries via ashlr__grep
• Backward compat: no discovery sections → empty list, grep behaves as Q1
• Full suite: 3033 pass / 0 fail / 1 skip
• bunx tsc --noEmit clean

Constraints honored

• No new external dependencies.
• Free tier never makes an LLM call (gated at function top, before any provider lookup).
• CLI-only — synthesizer never runs in a hook hot path; respects the 2s safety net.
• Cherry-picked cleanly off main.

🤖 Generated with Claude Code

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