chore(handoff): refresh to 26 connectors + standalone-audit-clean

.planning/.continue-here.md

@@ -1,99 +1,94 @@
 ---
 context: default
 project: Pinakes
-stage: Stage 3 Wave 3 COMPLETE (22 connectors); module renamed to pinakes.sh/pinakes; Wave 4 in flight
-status: stage-3-wave-3-complete-module-renamed
-head_commit: 9a76029
-last_updated: 2026-06-13
+stage: Stage 3 — 26 connectors (all codex-clean); module pinakes.sh/pinakes; standalone-release prep (Work Stream A) COMPLETE, audit CLEAN
+status: stage-3-26-connectors-standalone-audit-clean
+head_commit: 146c54d
+last_updated: 2026-06-14
 ---
 
-# Pinakes — Continue Here (Stage 3 Waves 1-3 + module rename done; Wave 4 in flight)
+# Pinakes — Continue Here (26 connectors; standalone-release audit CLEAN)
 
 You are the **core-build agent** for Pinakes (deterministic, verifiable data layer for AI agents;
 biology beachhead, arXiv literature LAST). Repo `/Users/tristanfarmer/Projects/operon`, `origin/main`
-= `github.com/001TMF/pinakes` (private, founder's PERSONAL account — NO org) @ `9a76029`.
-Build env: `export PATH="$PATH:/opt/homebrew/bin"`. **Module path `pinakes.sh/pinakes`** (renamed
-from the placeholder github.com/pinakes/pinakes in #47 — imports read `pinakes.sh/pinakes/...`).
-ULTRACODE is ON. `make ci` == the gate. A PR touching `engine/`/`idl/`/`schema/` needs the
-**`spine-change`** label (frozen-path CI guard). gh authed as 001TMF. codex CLI (gpt-5.5,
-ChatGPT-authed) is the cross-model gate.
+= `github.com/001TMF/pinakes` (private, founder's PERSONAL account — NO org) @ `146c54d`.
+Build env: `export PATH="$PATH:/opt/homebrew/bin"`. **Module path `pinakes.sh/pinakes`** (vanity import
+path, resolved via a go-import meta tag → github.com/001TMF/pinakes). ULTRACODE is ON. `make ci` == the
+gate. A PR touching `engine/`/`idl/`/`schema/` needs the **`spine-change`** label (frozen-path CI guard).
+gh authed as 001TMF. codex CLI (gpt-5.5, ChatGPT-authed) is the cross-model gate.
 
 ## Required reading
 1. `DECISIONS.md`, `CONTRACTS.md`, `BUILD_ROADMAP.md` (§3 = Stage-3 waves), `RESUME.md`.
-2. **`.planning/HANDOFF.json`** — machine state (may be stale on connector count; trust this file + git).
+2. **`.planning/HANDOFF.json`** — machine state (may lag on connector count; trust git: it's 26).
 3. `engine/contract/doc.go` — the canonical determinism/hash-purity contract (the connector build bar).
-4. `RELEASING.md` (repo root) — the founder-gate publish checklist (now incl. the go-import meta-page gate).
-5. `.planning/analysis/BLOAT-REPORT.md` — bloat analysis (verdict: lean; cleanup DEFERRED, see below).
+4. `RELEASING.md` — the founder-gate publish checklist (incl. the go-import meta-page gate).
+5. **`.planning/analysis/STANDALONE-DECOUPLING.md`** — the A1 standalone-release audit (verdict CLEAN).
+6. `.planning/analysis/BLOAT-REPORT.md` — bloat analysis (verdict lean; cleanup DEFERRED).
 
 ## Baseline
-`make ci` GREEN at `9a76029`. **22 connectors** live: alphafold, cbioportal, chembl, clinicaltrials,
-clinvar, complexportal*, ensembl, geneontology, gnomad, gtex, gwascatalog*, gtopdb*, hpo, interpro,
-jaspar, monarch, ncbidatasets, ncbiprotein, ncbivirus, openfda, opentargets, pdb, pubchem, reactome,
-rhea*, uniprot. (* = the 4 Wave-4 connectors are IN FLIGHT in worktree, not yet merged — see below.)
-NOTE: pre-existing FLAKY test in engine/governor (TestGovernor_Stress / InteractiveBeatsBatch,
-timing-sensitive under -race contention) — if `make ci`/CI fails ONLY on it, re-run; NOT connector-caused.
+`make ci` GREEN at `146c54d`. **26 connectors** live, ALL codex-clean: alphafold, cbioportal, chembl,
+clinicaltrials, clinvar, complexportal, ensembl, geneontology, gnomad, gtex, gtopdb, gwascatalog, hpo,
+interpro, jaspar, monarch, ncbidatasets, ncbiprotein, ncbivirus, openfda, opentargets, pdb, pubchem,
+reactome, rhea, uniprot. The engine/governor timing suite is DETERMINISTIC now (synctest, #49) — a
+governor failure is a REAL bug, not the old flake.
 
 <completed_work>
-- **Stages 0-2b COMPLETE** (engine spine, 3 surfaces MCP/CLI/REST, CI + signed-release pipeline). **Audit #1-#6 CLOSED.**
-- **Stage 3 Wave 1** (#33/#35/#39/#40 → 14): openfda, clinicaltrials, cbioportal, ncbidatasets. Bookend fix #44.
-- **Stage 3 Wave 2** (#45 → 18): reactome, gene-ontology(QuickGO), hpo, jaspar. The WIRE step made
-  provider_test.go's source-count assertions STRUCTURAL (`len(specs)==len(registry)` + floor) — so new
-  connector batches need NO count bump and never conflict on it. codex caught a real false-Complete in
-  EACH (bracket-the-whole-walk, body-id verify, empty-get-422, 204→UNKNOWN) — all fixed + regression-tested.
-- **Stage 3 Wave 3** (#46 → 22): opentargets(GraphQL), gtex, monarch(BioLink), interpro(EBI cursor). THREE
-  codex rounds (author≠verifier): round1 (trailing-empty-page total, search-filter verify, anchor-id,
-  empty-get, 204); round2 (gtex dataset-substitution, blank-filter-422, monarch Retrieve-layer empty-ids,
-  400→422); round3 (gtex+monarch honor plan-snapshot st.Reconcile not live c.reconcile). All fixed + non-vacuous
-  regression tests. Documented monarch's conservative acc!=id alias limitation (determinism-safe).
-- **MODULE RENAME** (#47): github.com/pinakes/pinakes → **pinakes.sh/pinakes** (vanity import path). Repo-URL
-  refs (install.sh PINAKES_REPO, README badges, RELEASING cosign-identity) → github.com/001TMF/pinakes
-  (cosign identity follows where release.yml RUNS, independent of module path). Stale pinakes.ai → pinakes.sh
-  in docs. RELEASING gained the go-import meta-page publish gate.
-- **Bloat analysis** (`.planning/analysis/BLOAT-REPORT.md`): codebase is LEAN (~700 removable Go lines +
-  ~1-1.3K doc lines). User chose **DEFER ALL** cleanup (see remaining_work).
+- **Stages 0-2b COMPLETE** (engine spine, 3 surfaces MCP/CLI/REST, CI + signed-release pipeline). Audit #1-#6 CLOSED.
+- **Stage 3 Waves 1-4 MERGED** (14→18→22→26): wave1 openfda/clinicaltrials/cbioportal/ncbidatasets; wave2
+  reactome/geneontology/hpo/jaspar; wave3 opentargets/gtex/monarch/interpro; wave4 gwascatalog/complexportal/
+  gtopdb/rhea. Each connector survived multi-round codex cross-model determinism audits + non-vacuous regression tests.
+- **MODULE RENAME** (#47): → `pinakes.sh/pinakes`. Repo-URL refs (install.sh, README, cosign identity) →
+  github.com/001TMF/pinakes (cosign identity follows where release.yml RUNS, independent of module path).
+- **Governor de-flake** (#49, spine-change): synctest; production .go byte-for-byte unchanged; 0 flakes / ~2900 -race iters.
+- **CODEX ROUND-4 DISCHARGED** (#51): the deferred Wave-4 final re-verify ran when quota reset — gtopdb NO DEFECTS;
+  complexportal HIGH found (two untrusted full-body decodes lacked an EOF check → false Complete / hash impurity) and
+  FIXED with `requireEOF` (mirrors gtopdb) + 2 non-vacuous regression tests (proven by revert).
+- **STANDALONE-RELEASE PREP — Work Stream A COMPLETE** (the user's objective: ship the engine standalone, add cloud
+  "as it grows"):
+  - **A1 decoupling audit → CLEAN** (`.planning/analysis/STANDALONE-DECOUPLING.md`): engine has ZERO cloud dependency;
+    build closure = stdlib + x/text + yaml + internal only; snapshot.Backend defaults to local FSBackend (cloud seam
+    NewStoreWithBackend inert); literature/arXiv ABSENT; no telemetry/phone-home; serve loopback-enforced; jobs in-process;
+    cold-start with scrubbed env works. NO decoupling code change needed.
+  - **A3 docs** (#52): README "Local state" section (default `<UserCacheDir>/pinakes` + `PINAKES_STATE_ROOT`). The
+    PINAKES_API_KEY-is-future-tier nit was already covered (README.md:225). README is already standalone-first.
 </completed_work>
 
 <remaining_work>
-- **GATE + MERGE Wave 4** (workflow `wrwkwkk18`, worktree `../pinakes-wt-wave4`, branch feat/wave4-batch):
-  building gwascatalog, complexportal, gtopdb (CC-BY-SA copyleft→served-live), rhea with a Wave-3-HARDENED
-  build bar (mandatory guards a-f baked in: trailing-empty-page total, search-filter verify, body-id/composite
-  verify, non-200-never-stored + 204→UNKNOWN, empty-get-422 at Plan AND Retrieve 3-way dispatch, plan-snapshot
-  reconcile). When done: review → per-connector codex gate (KEEP IT — it has caught a real bug in nearly every
-  connector) → fix any findings + regression tests → make ci → ONE PR (no spine-change label, connectors only) → merge.
-- **KEEP BREADTH GOING** (user directive: "make it quite large in a few workflows"): after Wave 4 merges, launch
-  Wave 5 off the updated main (reuse the wave4 workflow script, swap connectors). Roadmap remainder: STRING, Human
-  Protein Atlas (CC-BY-SA), MSigDB, Expression Atlas, IntAct, ChEBI, Bgee, GWAS-adjacent, Pharos, etc. (DepMap has
-  no clean REST — skip). Non-pathogen → fine in workflows; pathogen-DATA capture → main loop/codex (AUP).
-- **DEFERRED bloat cleanup** (user: DEFER ALL): do the 6-non-hash-helper extraction (readBody/backoff/jsonNumberOrNil/
-  toAnySlice/httpDoer/emptyToNil → connectors/internal/, ~700 lines) as ONE dedicated pass AFTER breadth settles
-  (it touches all connectors; spine-adjacent; gate behind golden-hash tests; do NOT touch the canonicalizer trio —
-  deliberately connector-local for hash isolation). Docs cleanup (vestigial Operon_*/RECONCILIATION) = pre-public prep (parked).
-- **INGEST-CLOUD COORDINATION**: the other agent (../provenir-ingest, branch feat/ingest-cloud) imports the engine.
-  After the rename they must update go.mod require/replace LHS → pinakes.sh/pinakes + sweep imports (seam types
-  snapshot.Backend / literature.PaperRecord UNCHANGED). Awaiting their reply on local-replace vs pinned consumption.
-- **MCP-prompt client-neutral key affordance** (tracked): add MCP `prompts` capability + a prompt that GUIDES the
-  user to run `pinakes config set-key` (returns instructions only). Spine-adjacent → spine-change label.
-- **FOUNDER GATES (PARKED — public can wait per user)**: go-import meta page at pinakes.sh/pinakes (needed for
-  `go install`; local replace + curl|sh unaffected); make repo public; get.pinakes.sh; npm/PyPI reserve; Homebrew
-  tap; branch/tag protection; USPTO/EUIPO check. **Stage 6 arXiv/literature = LAST.** Stage 4/5 = separate ../pinakes-cloud.
+- **A2 FOUNDER GATES (the user's — launch plumbing, cloud-independent; this is now the critical path to a PUBLIC release)**:
+  publish the go-import meta page at pinakes.sh/pinakes; make the repo public; stand up get.pinakes.sh; publish the
+  Homebrew tap + wire the goreleaser `brews:` block; tag **v0.1.0** (fires cosign-signed goreleaser); enable branch/tag
+  protection. (optional: npm/PyPI reserve, USPTO/EUIPO check.) Do NOT publish without the user.
+- **WORK STREAM B — KEEP BREADTH GOING (standing user directive: "make it quite large in a few workflows")**: launch
+  Wave 5 off main, reusing the wave4 batch script (`.claude/.../workflows/scripts/wave4-connector-batch-wf_c6f2836d-b00.js`
+  — swap the connector list; it bakes in the HARDENED build bar incl. the requireEOF/EOF rule). Candidates (non-pathogen,
+  clean public APIs): STRING, Human Protein Atlas (CC-BY-SA → served-live), MSigDB, Expression Atlas, IntAct, ChEBI, Bgee,
+  Pharos (DepMap has no clean REST — skip). Structural provider count test → parallel batches don't conflict. Non-pathogen
+  → fine in workflows; pathogen-DATA capture → main loop/codex (AUP). KEEP the per-connector codex gate; pace codex (quota).
+- **DEFERRED bloat cleanup** (user: DEFER ALL): the 6-non-hash-helper extraction (readBody/backoff/jsonNumberOrNil/
+  toAnySlice/httpDoer/emptyToNil → connectors/internal/, ~700 lines) as ONE post-breadth pass; gate behind golden-hash
+  tests; do NOT touch the per-connector canonicalizer trio. (.planning/analysis/BLOAT-REPORT.md.)
+- **INGEST-CLOUD COORDINATION**: ../provenir-ingest (branch feat/ingest-cloud) imports the engine; after the rename it must
+  update go.mod require/replace LHS → pinakes.sh/pinakes + sweep imports (seam types snapshot.Backend / literature.PaperRecord
+  UNCHANGED). Awaiting their reply on local-replace vs pinned consumption.
+- **MCP-prompt client-neutral key affordance** (tracked): add MCP `prompts` capability + a prompt that GUIDES the user to
+  run `pinakes config set-key` (instructions only). Spine-adjacent → spine-change label.
+- **Stage 6 arXiv/literature = LAST.** Stage 4/5 cloud = the separate ../pinakes-cloud repo (plugs in behind snapshot.Backend).
 </remaining_work>
 
 ## Rhythm (keep it)
-design/research → implement via a Workflow (build → 3-lens adversarial Claude review [determinism/contract/test-rigor]
-→ fix) → **codex gpt-5.5 cross-model gate** (`printf '%s' "$P" | codex exec -m gpt-5.5 -s read-only`; bounded with a
-`( sleep ~300; kill $pid )&` watchdog; non-blocking; catches real determinism/credential bugs the Claude lenses miss —
-INVALUABLE, keep on every connector) → fix findings + non-vacuous regression tests (prove by revert) → personal `make ci`
-→ PR (`gh pr create --body-file`; +`--label spine-change` for engine/idl/schema) → merge `--merge --delete-branch` on
-GREEN CI. Author≠verifier. AUTO-MERGE ON GREEN authorized. The recurring codex classes are now in the Wave-4 build bar.
+research → implement via a Workflow (build → 3-lens adversarial Claude review [determinism/contract/test-rigor] → fix) →
+**codex gpt-5.5 cross-model gate** (`printf '%s' "$P" | codex exec -m gpt-5.5 -s read-only`; bounded with a
+`( sleep ~300; kill $pid )&` watchdog; catches real determinism bugs the Claude lenses miss — it found a HIGH in complexportal
+at ROUND 4 that 3 Claude reviews missed; KEEP IT on every connector) → fix + non-vacuous regression tests (prove by revert) →
+personal `make ci` → PR (`gh pr create --body-file`; +`--label spine-change` for engine/idl/schema) → merge `--merge
+--delete-branch` on GREEN CI. Author≠verifier. AUTO-MERGE ON GREEN authorized.
 
 ## Environment gotchas
 - EXPLICIT `git add <files>`, NEVER `git add -A`. `.planning/*` gitignored except `.continue-here.md` + `HANDOFF.json`.
 - DIRECT PUSH TO main BLOCKED by the auto-mode classifier — even docs/handoff go via branch + PR.
-- zsh: unquoted `$VAR` no word-split; `$pipestatus` not `$PIPESTATUS`; `gh --body-file` (backticks in `--body` run subst).
+- zsh: `$pipestatus` not `$PIPESTATUS`; `gh --body-file` (backticks in `--body` run subst).
 - macOS: no `timeout` (use `( sleep N; kill $pid )&`). `sed -i ''` (empty arg). The `cannot delete local branch … used by
-  worktree` on `gh pr merge --delete-branch` is benign — remote+local deleted; `git worktree remove <wt> --force` after.
-- codex: pipe the prompt via stdin (positional-arg prompt hangs on stdin). Run the gate as a background bash script
-  looping the connectors sequentially; grep the output for severities when done.
+  worktree` on `gh pr merge --delete-branch` is benign — `git worktree remove <wt> --force` after.
+- codex: pipe the prompt via stdin (positional hangs); heavy use exhausts the ChatGPT quota (resets a few hrs later).
 - This repo = downloadable ENGINE only. cloud/ingest = the separate `../pinakes-cloud` (../provenir-ingest) repo.
-- Two strings in play forever: MODULE/import path = `pinakes.sh/pinakes`; REPO URL (download/CI/cosign) =
-  `github.com/001TMF/pinakes`. Never conflate them in install.sh / goreleaser / README / docs.
+- Two strings forever: MODULE/import path = `pinakes.sh/pinakes`; REPO URL (download/CI/cosign) = `github.com/001TMF/pinakes`.

.planning/HANDOFF.json

@@ -1,12 +1,12 @@
 {
-  "version": "1.3",
-  "timestamp": "2026-06-13",
+  "version": "1.4",
+  "timestamp": "2026-06-14",
   "project": "Pinakes",
-  "stage": "Stage 3 Wave 1 COMPLETE (14 connectors); audit #1-#6 ALL closed; LICENSE/SECURITY/RELEASING + optional API keys landed; agent skill in flight. See .planning/.continue-here.md for the authoritative current narrative.",
-  "status": "stage-3-wave-1-complete",
-  "head_commit": "beff063",
+  "stage": "Stage 3 — 26 connectors live, ALL codex-clean (Waves 1-4 merged); module renamed to pinakes.sh/pinakes; governor de-flaked (synctest); standalone-release prep (Work Stream A) COMPLETE with the A1 decoupling audit CLEAN. See .planning/.continue-here.md for the authoritative current narrative.",
+  "status": "stage-3-26-connectors-standalone-audit-clean",
+  "head_commit": "146c54d",
   "origin": "github.com/001TMF/pinakes (private)",
-  "module_path": "github.com/pinakes/pinakes",
+  "module_path": "pinakes.sh/pinakes",
   "build_env": "export PATH=\"$PATH:/opt/homebrew/bin\"",
   "baseline_green": "go build ./... && go test ./... -race -count=1 GREEN at 8a3e9f9; binary: go build -o /tmp/pinakes ./cmd/pinakes",
   "completed": [