Glean Health -- Dev Status

GEMINI Principle #2 banned "symptom" from patient UI (euphemize as Signals/Experiences); superseded because it wasn't guard-enforced, no patient code used a euphemism, and "symptom" is plain searchable English serving Discoverability (#4) better — the non-advice stance is carried by the glass-box signal band, not by avoiding the word. Edited `GEMINI.md` + `web/GEMINI.md` + `docs/PHYSICAL_SCHEMA.md`. Also retired Principle #1 "Conditions & Remedies Only" → **three entry vectors** (condition / remedy / symptom). Patient nav route will be `/symptom/[slug]` (2026-06-19)

The raw `symptoms_targeted[]` vocabulary (~33.6k free-text strings, 79% ≤2 mentions) was too noisy to navigate. `extract/normalize_symptoms.py` canonicalizes it via Haiku (`claude -p`, Max plan — no API key configured) into **7,515 labels** (`data/symptom_canonical_map.json`). **Key structural insight: target-type is contextual, not intrinsic** (the same string `mcas` is a degenerate self-reference inside the MCAS corpus but a real comorbid treatment-target inside POTS). Hence three layers: (L1) normalize = context-free, canonicalize + type (symptom/sign/condition kept; trigger/other dropped), NEVER drops a condition-name; (L2) `migrate` drops self-references (target == own condition, type=condition only) using condition context; (L3) frontend decides surfacing. Per-canonical type resolved deterministically (exact-match-raw wins). `type` column cascaded through glean.db/web.db/`physical_schema.sql`/`schema_postgres.sql`/`push_to_supabase.py`/`PHYSICAL_SCHEMA.md`/`ARCHITECTURE.md`. All 9 guards green (2026-06-19)

Patient surface restyled to the "warm terminal" theme: monospace, greige ground, sage/ochre/clay earth tones (Jackson Browne palette). Token set + remap layer in `web/src/app/globals.css`; signal-band tags/stripes consume the same tokens. Live 2026-06-15 (commit `15e4a88`)

A condition can have 1,000+ treatments; mounting that many interactive cards buried the main thread (sluggish cursor, slow drilldowns). `web/src/app/condition/[id]/RemedyList.tsx`: progressive disclosure, `PAGE=50` by signal, reveal-on-demand. Full list held in memory (cheap JSON) so "Show more" is instant — only DOM/hydration cost is capped, the actual bottleneck. Deep links (Vector 2) beyond the first page widen the initial window so the `#tx-<id>` anchor + highlight still render (commit `c898588`, 2026-06-14)

Replaces any implied efficacy score with a signal-of-credible-discussion band that executes the product thesis (conversation-starter, never a verdict). `web/src/lib/signal.ts`: `signalBand(cluster_weight)` → Strong (≥20) / Moderate (≥6) / Emerging tiers, each an ASCII bar + earth-tone tinted tag + left stripe; thresholds grounded in the real corpus distribution (16,572 treatments, p75≈6, p95≈22 → Strong≈top 5%, Moderate≈p75–p95). `researchContext(pubmed_count)` reframes PubMed coverage as a doctor-conversation cue (well/some/barely/not-yet studied), surfacing the "community ahead of the science" gap as honest context, not a headline. Applied to Vectors 1 & 2 (commit `5930db0`, 2026-06-14)

Magic-link UX confused testers and free-tier Supabase email (Yahoo spam, low rate limit) was a deliverability wall; bouncing between localhost and prod added redirect-allow-list friction. Swapped `signInWithOtp` → `signInWithPassword` (`web/src/app/login/page.tsx`) and deleted the now-dead `/auth/confirm` magic-link callback. Invite-only preserved via admin-provisioned accounts (Supabase Users, password + Auto Confirm) — no public sign-up, no email at login. Session/`proxy.ts` unchanged (same cookie flow). Magic-link prose swept from CLAUDE.md / ARCHITECTURE.md / OVERVIEW.md. Live 2026-06-14 (2026-06-14)

Triggered by a full repo audit ("clean / coupled / referenced") run via parallel read-only subagents + the 8-guard sweep. Verdict: repo fundamentally healthy (tree clean, 8 guards <!-- count-ok --> green, `web/` app fully Postgres-migrated, no markers/conflicts/half-done code, PLAN/RUNBOOK hygienic); the remaining staleness was almost entirely #46's deferred bucket. Closed it: (1) **CLAUDE.md** — rewrote "Dev vs Patient Surfaces" as a PHYSICAL split (patient = `web/` Vercel app on Supabase; dev = Cloudflare static, bare domain redirects to `dev.html`); removed the 5 archived-stack rows from the Project Structure table; fixed the §"Coupled Artifacts" `deploy/index.html`→`deploy/pipeline.html` renderer refs. (2) **ARCHITECTURE.md** (~14 current-prose sites) + **OVERVIEW.md** reconciled by a subagent (dated change-log entries left as history); also fixed OVERVIEW §2.3 "Seven scripts"→"Eight" + added the `check_serving_freshness` row (a 7→8 gap `check_live_counts` can't see — "scripts" not "guards"). (3) **`build_dev_status.py`** dev-nav "Patient site → /" repointed to the Vercel app + JS active-tab default `index.html`→`dev.html`; propagated to the 6 committed dev pages via `inject_dev_nav.py` + regen. (4) **`extract/build_ui.py`** Project Files entry + Browse crumb repointed to the Vercel app (re-rendered all 26 dashboards to clear the resulting `check_manifest` STALE). Non-#46 audit finds also fixed: `PHYSICAL_SCHEMA.md` stale "app reads web.db" → loader; `.gitignore` 6.1→6.5 GB; 3 orphan root `test_*.py` → `tests/`; 4 info `console.log`s removed from `web/`; obsolete `decisions.yaml` TODO marked moot. NOTE: regenerating `corpus.html` for the nav also picked up an **overdue deterministic data refresh** (committed copy was stale vs current pipeline outputs: mentions 133190→133230, clusters 16568→16572) — legit, not guard-tracked. All 8 guards <!-- count-ok --> green (2026-06-12)

Per the 2026-06-12 priority reset (pipeline preservation > frontend), closed the "memory-bridged gap": `run_condition.py` stops at the JSON pipeline outputs and never touches Supabase, so a finished run silently left the live app serving stale data. Three moves: (1) **`scripts/refresh_serving.py`** — one-command orchestrator for the serving chain (migrate → `build_web_db` → `push_to_supabase`), with fail-fast prechecks (pipeline outputs exist, `web/.env.local` present) and a prod-reload confirmation; on success writes `data/serving_manifest.json` (condition → sha256 of pipeline output; gitignored, machine-local). Flags: `--yes`, `--skip-rebuild`, `--record-only`. (2) **`scripts/check_serving_freshness.py`** — guard #8, compares the manifest to current pipeline outputs and flags STALE/NEW/REMOVED; wired into `dev_status.html` via `build_dev_status.py` GUARDS; verified it catches all three drift types (exit 1) and passes clean (exit 0). (3) **`docs/RUNBOOK.md`** — the single end-to-end "build half + publish half" runbook; `run_condition.py` now prints a "NEXT: publish" reminder on completion. Baselined the manifest via `--record-only` (Supabase already in sync — no pipeline re-runs since the last push). Guard count 7→8 (CLAUDE.md, OVERVIEW.md ×3, PLAN.md ×2 reconciled; `check_live_counts` enforces). This also resolved the onboarding-checklist item from #46's deferred list (CLAUDE.md §94 now points at `refresh_serving.py` + RUNBOOK and drops the archived `build_home.py`); the rest of #46's frontend reconciliation stays deferred (2026-06-12)