feat(openontology): Phase 2 + Phase 3 — storage, REST/SSE, MCP, RDF/SHACL, adapters, TUI, explorer (#101)

Everything the two shipped PRD phases deferred, minus what is called out below.

Storage (Phase 2)
  @logicsrc/openontology gains a SQLite/Turso adapter. It hydrates the read
  model at open, serves reads synchronously — a query evaluator that awaits per
  triple pattern is unusable — and buffers mutations as SQL that flush() writes
  in one transaction. Versioned idempotent migrations; indexes over subject,
  predicate, entity-valued object, status, both time axes, aliases, and external
  ids; FTS5 for label/alias search. The append-only status log is replayed on
  open, so retractions, supersessions, and merge redirects survive a reopen.

REST + SSE + OpenAPI (Phase 2)
  16 paths under /api/ontologies in logicsrc-web, described at
  /api/ontologies/openapi and referencing the published JSON Schemas rather
  than restating them. No token is read-only; a curator token can apply; an
  agent token can propose and cannot apply. Idempotency-Key on mutations,
  revision ETags, 409 on a stale base revision, and an SSE stream that emits
  the same event objects as the JSON endpoint.

MCP (Phase 2)
  OpenOntology and OpenPRD surfaces on the standards server: spec/manifest/
  schema/queries and PRD spec/index as resources, 11 ontology tools and 6 PRD
  tools, 7 prompts. Read-only by default; OPENONTOLOGY_MCP_WRITABLE=1 buys
  proposals, never applies — the denial is the shared policy layer, not a
  second rule that could drift.

Interoperability (Phase 3)
  RDF/Turtle export and import of the reified profile, plus the plain triple
  for asserted relationships so a consumer wanting only the accepted graph gets
  one. SHACL for 5 of 7 constraint kinds; `unique` and `query` are reported as
  unmapped in both the return value and the generated Turtle, because a shape
  that quietly means something narrower is worse than no shape.

Source adapters (Phase 3)
  CSV, JSON, YAML, NDJSON, Markdown, generic JSON HTTP, and GitHub. All produce
  PROPOSED change-set operations with source, evidence selector, run id, and
  confidence attached; fetch is injected so ingestion is offline and testable.
  Each declares its capabilities, so "nothing was deleted upstream" is never
  confused with "this adapter cannot see deletions" — none of the seven can.

TUI + explorer
  Keyboard-first panels (types, entities, claims, sources, queries, change
  sets, validation, audit) as plain strings that survive SSH and 60 columns;
  status is a glyph and a word, never colour alone; the key bar wraps rather
  than truncating. Wired as `logicsrc ontology tui`. A read-only web explorer
  at /openontology/explore with entity and claim views showing status, both
  clocks, confidence, sources, evidence, and append-only history — plus an
  /openprd page for the companion standard.

Bugs found and fixed while testing
  - the API built a new engine per request, so `explain` could never find a
    resultId from a prior request; engines are now cached per role
  - the TUI status bar called engine.validateOntologyPackage(), appending a
    package.validated event on every repaint; it now uses the pure validator

Verification: 76 new tests (527 total across the monorepo, all passing); full
build green; the libSQL adapter is exercised against real files, the API
through its route handlers, and MCP over an in-memory transport.

Not included: PWA review/approval write flows (they need an auth story this
deployment does not have), OWL/RDFS mappings, SPARQL/Cypher/Datalog query
adapters, and Phase 4 governed actions. The compatibility matrix marks those
"planned", not "supported".

Refs: prd/0001-add-logicsrc-openontology-spec.md

Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>

packages/tui/src/openontology.test.ts

@@ -0,0 +1,94 @@
+import { mkdtempSync, rmSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { afterAll, describe, expect, it } from "vitest";
+import {
+  createOntologyEngine,
+  initOntologyPackage,
+  loadOntologyPackage,
+  localActor
+} from "@logicsrc/openontology";
+import { renderOntologyKeyHelp, renderOntologyTui, PANEL_KEYS } from "./openontology.js";
+
+const dirs: string[] = [];
+afterAll(() => {
+  for (const dir of dirs) rmSync(dir, { recursive: true, force: true });
+});
+
+function engine() {
+  const dir = mkdtempSync(join(tmpdir(), "tui-ontology-"));
+  dirs.push(dir);
+  initOntologyPackage(dir, { id: "test-ecosystem", now: "2026-07-26T00:00:00Z" });
+  return createOntologyEngine({
+    package: loadOntologyPackage(dir),
+    actor: localActor("curator"),
+    clock: () => "2026-07-26T00:00:00Z"
+  });
+}
+
+describe("ontology TUI", () => {
+  it("renders a bordered frame with the key bar and status line", () => {
+    const output = renderOntologyTui(engine());
+    const lines = output.split("\n");
+    expect(lines[0]!.startsWith("┌")).toBe(true);
+    expect(lines.at(-1)!.startsWith("└")).toBe(true);
+    expect(output).toContain("e entities");
+    expect(output).toContain("q quit");
+    expect(output).toContain("asserted claims");
+  });
+
+  it("never exceeds the requested width, and stays usable when narrow", () => {
+    for (const width of [60, 78, 120]) {
+      const lines = renderOntologyTui(engine(), { width }).split("\n");
+      const widths = new Set(lines.map((line) => [...line].length));
+      expect(widths.size).toBe(1);
+      expect([...widths][0]).toBe(Math.max(width, 60));
+    }
+  });
+
+  it("shows every panel", () => {
+    const e = engine();
+    expect(renderOntologyTui(e, { panel: "types" })).toContain("Person");
+    expect(renderOntologyTui(e, { panel: "entities" })).toContain("Alice Reyes");
+    expect(renderOntologyTui(e, { panel: "claims" })).toContain("worksOn");
+    expect(renderOntologyTui(e, { panel: "sources" })).toContain("web-page");
+    expect(renderOntologyTui(e, { panel: "queries" })).toContain("contributors");
+    expect(renderOntologyTui(e, { panel: "changesets" })).toContain("no change sets");
+    expect(renderOntologyTui(e, { panel: "violations" })).toContain("no errors");
+    expect(renderOntologyTui(e, { panel: "audit" })).toContain("no events");
+    // Rendering is read-only: repainting must not append to the audit log.
+    expect(renderOntologyTui(e, { panel: "audit" })).toContain("no events");
+  });
+
+  it("distinguishes claim status by glyph and word, not colour", () => {
+    const claims = renderOntologyTui(engine(), { panel: "claims", rows: 20 });
+    expect(claims).toMatch(/✓ asserted/);
+    // No ANSI escapes: the panel must survive a monochrome terminal.
+    expect(claims.includes("[")).toBe(false);
+  });
+
+  it("surfaces proposed change sets and disputes in the status bar", () => {
+    const e = engine();
+    e.createOntologyChangeSet({
+      title: "pending",
+      operations: [
+        {
+          op: "assert-claim",
+          value: {
+            subject: "test:person:alice",
+            predicate: "worksOn",
+            object: { entity: "test:project:docs-portal" },
+            sources: ["test:source:repo"]
+          }
+        }
+      ]
+    });
+    expect(renderOntologyTui(e)).toContain("1 proposed");
+    expect(renderOntologyTui(e, { panel: "changesets" })).toContain("pending");
+  });
+
+  it("lists the keys it binds", () => {
+    expect(renderOntologyKeyHelp()).toContain("v: validate");
+    expect(PANEL_KEYS.map((entry) => entry.key)).toContain("q");
+  });
+});