Atlas seed-harvest pipeline (Tier 1-3, approval artifact, sync)

[jpr5]

Summary

Adds the Atlas seed-harvest pipeline end to end:

• Leaf adapters (Tier 1) — seven per-source adapters (GitHub PR/issue, memory files, source comments, Notion docs, Linear docs, episodic transcripts via the LLM distill seam, showcase manifests) with shared credential/GTM sensitivity scanning and fail-loud intake guards.
• Pipeline stages (Tier 2-3) — aggregate (NUL-keyed fragment identity, cluster fusion, dedup-collapse reconciliation), classify (flag-set finalization), canonicalize (claim slugs with non-ASCII discriminators, canonical keys, rank scoring, supersession).
• Gates — deterministic + english-rule exclusion engine (LLM-judged, fail-closed), RAG-corpus dedup gate (mark-only, byte-budgeted probes, fail-fast streak), §7 source/showcase validation (errno-triaged checkout grep, feature-registry oracle).
• Approval artifact — Notion review page generation (flag badges, canonical-key markers, batch budgets, surrogate-safe rich text) and sync enactment (badge round-trip, checked-row exclusion judgment, idempotent 409 handling, §11.5 cross-run rule persistence).
• Wiring — webhook PR seeding, Atlas HTTP client, atlas-harvest CLI driver, CI prettier coverage.

Code review

Driven through a 13-round multi-agent CR loop (16 reviewers per round across code-review, silent-failure, test-coverage, comment-accuracy, and type-design lenses), with 12 fix rounds (fix2–fix13). Behavioral must-fix trajectory over the final rounds: 8 → 4 → 2 → 0, certified at R13 (folds-only final round verified by an exhaustive diff-audit gate). Full found/fixed/deferred audit manifests are retained locally (~/.claude/specs/2026-06-09-atlas-r*.md).

Accepted residuals (deliberate deferrals)

Documented per-line in the R13 manifest §f; headline classes: HTTP/LLM client timeouts, 409 idempotency detection by substring, empty-date fallbacks (??), non-atomic manifest writes, hand-mirrored enum sets, heuristic distillation/capture tuning (markdown edge cases), non-Latin tokenization in the dedup gate (mark-only), symlink blind spots in the validation walk, and S20-coupled items (/api/search route, webhook key-grammar unification, cross-run key stability under fusion).

Test plan

• Full suite: 5829/5829 across 320 files (vitest)
• tsc --noEmit clean on both configs (build + scripts)
• npm run build green
• Webhook byte-equivalence oracle green (B2)
• NUL-byte identity pin intact (hexdump-verified across 11 review rounds)
• CI green on this PR