v0.40.6.0 Phase 5+6+7 — schema lint with rich rules + 9 new MCP ops

This is the marquee commit: Wintermute and any other remote OAuth agent
can now author + introspect schema packs over normal HTTPS MCP. Phases
5+6 collapse into Phase 7 because the new MCP ops compose Phase 1.5's
lint rules and Phase 2/3's mutation/stats/sync cores directly — no
extra extraction needed (D6 from /plan-eng-review).

Phase 5: schema lint CLI wired to runAllLintRules from Phase 1.5
  Replaces the prior 2-rule check (duplicate names + missing prefix)
  with the full 11-rule suite. New --with-db flag opts into the 2
  DB-aware rules (extractable_empty_corpus, mutation_count_anomaly).
  JSON envelope shape stable. Exit code 1 on any error.

Phase 7: 9 new MCP operations
  Read-scope (NOT localOnly — read scope is safe to expose remote):
    get_active_schema_pack — identity packet (pack name, sha8, counts).
    list_schema_packs       — bundled + installed names.
    schema_stats            — composes runStatsCore from Phase 3.
    schema_lint             — composes runAllLintRules; --with-db is
                              CLI-only (DB-aware rules need engine).
    schema_graph            — JSON {nodes, edges} from link_types
                              inference + frontmatter_links.
    schema_explain_type     — settings for one declared type.
    schema_review_orphans   — untyped pages drilldown.
  Admin-scope (NOT localOnly per D2 — Wintermute reaches via OAuth):
    schema_apply_mutations  — BATCHED per D10. Single MCP tool taking
                              a mutations[] array; composes all 11
                              mutate primitives. Atomic batch_id; outer
                              withPackLock wraps the whole batch so no
                              other writer can slip in mid-iteration.
                              Partial-results returned on mid-batch
                              failure for forensic agent debugging.
                              Audit log records actor=mcp:<clientId8>
                              (D20 privacy-redacted shape).
    reload_schema_pack      — flush in-process cache + extends-chain
                              cascade (codex C6 fix from Phase 1.3).

withConnectedEngine defensive fix applied to schema.ts:withConnectedEngine
  (PR #1321 closed) — EngineConfig built once and passed to BOTH
  createEngine AND engine.connect for defense in depth.

Test seams:
  - operationsByName lookup pinned for every new op.
  - All 9 ops have scope + localOnly declarations pinned to lock in
    the trust posture.
  - Batched mutation atomicity tested: partial-failure returns
    {error: mutation_failed, partial_results: [...]} with one batch_id
    across all results.
  - Audit log actor=mcp:<clientId.slice(0,8)> capture verified
    end-to-end (audit JSONL read back after the op handler runs).
  - Empty mutations[] rejected with invalid_request.
  - Unknown op surfaced via SchemaPackMutationError INVALID_RESULT.

Coverage: 23 new cases for the 9 ops (operations-schema-pack.test.ts).
All 255 schema-pack-related tests green.

Plan: ~/.claude/plans/system-instruction-you-are-working-recursive-thacker.md
Successor to: closed PR #1321.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/commands/schema.ts

@@ -692,6 +692,7 @@ async function runGraphCmd(args: string[]): Promise<void> {
 
 async function runLintCmd(args: string[]): Promise<void> {
   const { json, positional } = parseFlags(args);
+  const withDb = args.includes('--with-db');
   const name = positional[0];
   const cfg = loadConfig();
   let pack: SchemaPackManifest | null;
@@ -705,25 +706,33 @@ async function runLintCmd(args: string[]): Promise<void> {
     console.error(`Pack not found: ${name}`);
     process.exit(1);
   }
-  const warnings: string[] = [];
-  const seenTypeNames = new Set<string>();
-  for (const t of pack.page_types) {
-    if (seenTypeNames.has(t.name)) warnings.push(`duplicate type name: ${t.name}`);
-    seenTypeNames.add(t.name);
-    if (!t.path_prefixes || t.path_prefixes.length === 0) {
-      warnings.push(`type \`${t.name}\` has no path_prefixes — unreachable by inferType`);
-    }
-  }
+  // v0.40.6.0 Phase 5: swap basic 2-rule check for the rich 11-rule lint
+  // suite from Phase 1.5. File-plane rules run by default; --with-db
+  // opts into extractable_empty_corpus + mutation_count_anomaly which
+  // need an engine connection.
+  const { runAllLintRules } = await import('../core/schema-pack/lint-rules.ts');
+  const report = withDb
+    ? await withConnectedEngine(async (engine) => runAllLintRules(pack!, { engine }))
+    : await runAllLintRules(pack);
   if (json) {
-    console.log(JSON.stringify({ schema_version: 1, pack: pack.name, warnings }, null, 2));
+    console.log(JSON.stringify({ schema_version: 1, pack: pack.name, ...report }, null, 2));
+    if (!report.ok) process.exit(1);
     return;
   }
-  if (!warnings.length) {
+  if (report.ok && report.warnings.length === 0) {
     console.log(`OK — pack \`${pack.name}\` lint clean.`);
     return;
   }
   console.log(`Pack \`${pack.name}\` lint:`);
-  for (const w of warnings) console.log(`  warn: ${w}`);
+  for (const e of report.errors) {
+    console.log(`  ERROR (${e.rule}): ${e.message}`);
+    if (e.hint) console.log(`    hint: ${e.hint}`);
+  }
+  for (const w of report.warnings) {
+    console.log(`  warn (${w.rule}): ${w.message}`);
+    if (w.hint) console.log(`    hint: ${w.hint}`);
+  }
+  if (!report.ok) process.exit(1);
 }
 
 async function runExplainCmd(args: string[]): Promise<void> {

src/core/operations.ts

@@ -3801,6 +3801,359 @@ async function getRemoteMaxBytes(engine: BrainEngine): Promise<number> {
 
 // --- Exports ---
 
+// ──────────────────────────────────────────────────────────────────────
+// v0.40.6.0 Schema Cathedral v3 — 9 new MCP ops for the agent on-ramp.
+//
+// Read ops (scope: read; NOT localOnly) — any read-scope OAuth client.
+// Write ops (scope: admin; NOT localOnly per D2) — admin-scope client
+// (Wintermute and similar remote agents) can author schema packs
+// remotely. Audit log captures actor=mcp:<clientId8> on every mutation
+// (see src/core/schema-pack/mutate-audit.ts privacy posture per D20).
+//
+// Per-call schema_pack opt STAYS rejected for remote callers — that
+// trust boundary is enforced by op-trust-gate.ts and is separate from
+// the localOnly posture (R2 regression preserved).
+// ──────────────────────────────────────────────────────────────────────
+
+const get_active_schema_pack: Operation = {
+  name: 'get_active_schema_pack',
+  description: 'v0.40.6.0: cheap identity packet for the active schema pack. Returns {pack_name, version, sha8, page_types_count, link_types_count, primitive_summary, source_tier}. Useful for agents to know which pack they are operating against without paying full manifest load cost.',
+  params: {},
+  scope: 'read',
+  handler: async (ctx) => {
+    const { loadActivePack, resolveActivePackNameOnly } = await import('./schema-pack/load-active.ts');
+    const { loadConfig } = await import('./config.ts');
+    const cfg = loadConfig();
+    const sourceOpts: Record<string, unknown> = {};
+    if (ctx.sourceId) sourceOpts.sourceId = ctx.sourceId;
+    const resolution = resolveActivePackNameOnly({ cfg, remote: ctx.remote ?? true, ...sourceOpts });
+    const pack = await loadActivePack({ cfg, remote: ctx.remote ?? true, ...sourceOpts });
+    const primitiveSummary: Record<string, number> = {};
+    for (const t of pack.manifest.page_types) {
+      primitiveSummary[t.primitive] = (primitiveSummary[t.primitive] ?? 0) + 1;
+    }
+    return {
+      pack_name: pack.manifest.name,
+      version: pack.manifest.version,
+      sha8: pack.manifest_sha8,
+      identity: pack.identity,
+      page_types_count: pack.manifest.page_types.length,
+      link_types_count: pack.manifest.link_types.length,
+      primitive_summary: primitiveSummary,
+      source_tier: resolution.source,
+    };
+  },
+};
+
+const list_schema_packs: Operation = {
+  name: 'list_schema_packs',
+  description: 'v0.40.6.0: list installed schema packs (bundled + user-installed). Returns {bundled: string[], installed: string[]}. Read-only directory listing.',
+  params: {},
+  scope: 'read',
+  handler: async (_ctx) => {
+    const { existsSync, readdirSync } = await import('node:fs');
+    const { join } = await import('node:path');
+    const { gbrainPath } = await import('./config.ts');
+    const bundled = ['gbrain-base', 'gbrain-recommended'];
+    const installedDir = gbrainPath('schema-packs');
+    const installed: string[] = [];
+    if (existsSync(installedDir)) {
+      for (const entry of readdirSync(installedDir)) {
+        const candidates = ['pack.yaml', 'pack.yml', 'pack.json'];
+        for (const c of candidates) {
+          if (existsSync(join(installedDir, entry, c))) { installed.push(entry); break; }
+        }
+      }
+    }
+    return { bundled, installed };
+  },
+};
+
+const schema_stats: Operation = {
+  name: 'schema_stats',
+  description: 'v0.40.6.0: per-type page counts + typed-coverage from the DB. Returns {schema_version:1, pack_identity, aggregate, per_source, dead_prefixes}. Multi-source aware via ctx.sourceId/allowedSources.',
+  params: {},
+  scope: 'read',
+  handler: async (ctx) => {
+    const { runStatsCore } = await import('./schema-pack/stats.ts');
+    const scope = sourceScopeOpts(ctx);
+    const opts: { sourceId?: string; sourceIds?: string[] } = {};
+    if (scope.sourceIds && scope.sourceIds.length > 0) opts.sourceIds = scope.sourceIds;
+    else if (scope.sourceId) opts.sourceId = scope.sourceId;
+    return runStatsCore(ctx, opts);
+  },
+};
+
+const schema_lint: Operation = {
+  name: 'schema_lint',
+  description: 'v0.40.6.0: lint the active (or named) schema pack. File-plane rules only over MCP — the with_db option is rejected for remote callers (DB-aware rules require local CLI). Returns {ok, errors, warnings} structured report.',
+  params: {
+    pack: { type: 'string', description: 'Pack name (default: active pack)' },
+  },
+  scope: 'read',
+  handler: async (ctx, p) => {
+    const { runAllLintRules } = await import('./schema-pack/lint-rules.ts');
+    const { loadActivePack } = await import('./schema-pack/load-active.ts');
+    const { loadConfig, gbrainPath } = await import('./config.ts');
+    const { existsSync } = await import('node:fs');
+    const { join } = await import('node:path');
+    const cfg = loadConfig();
+    let manifest;
+    if (p.pack) {
+      // Locate by name without trust-gating per-call schema_pack opt
+      // (that's a separate axis — this is just file lookup).
+      const packName = p.pack as string;
+      const candidates = ['pack.yaml', 'pack.yml', 'pack.json'];
+      let path: string | null = null;
+      for (const c of candidates) {
+        const candidate = join(gbrainPath('schema-packs', packName), c);
+        if (existsSync(candidate)) { path = candidate; break; }
+      }
+      if (!path) return { error: 'pack_not_found', pack: packName };
+      const { loadPackFromFile: loader } = await import('./schema-pack/loader.ts');
+      manifest = loader(path);
+    } else {
+      const resolved = await loadActivePack({ cfg, remote: ctx.remote ?? true, sourceId: ctx.sourceId });
+      manifest = resolved.manifest;
+    }
+    // File-plane only over MCP; the engine-aware --with-db opt-in is
+    // CLI-only (Phase 5 wiring). MCP callers get the 9 file-plane rules.
+    return await runAllLintRules(manifest);
+  },
+};
+
+const schema_graph: Operation = {
+  name: 'schema_graph',
+  description: 'v0.40.6.0: schema pack graph as JSON edges. Returns {nodes: [{name, primitive}], edges: [{from, verb, to}]} derived from link_types inference + frontmatter_links.',
+  params: {},
+  scope: 'read',
+  handler: async (ctx) => {
+    const { loadActivePack } = await import('./schema-pack/load-active.ts');
+    const { loadConfig } = await import('./config.ts');
+    const cfg = loadConfig();
+    const pack = await loadActivePack({ cfg, remote: ctx.remote ?? true, sourceId: ctx.sourceId });
+    const nodes = pack.manifest.page_types.map((t) => ({ name: t.name, primitive: t.primitive }));
+    const edges: Array<{ from: string; verb: string; to: string }> = [];
+    for (const lt of pack.manifest.link_types) {
+      if (lt.inference?.page_type) {
+        edges.push({
+          from: lt.inference.page_type,
+          verb: lt.name,
+          to: lt.inference.target_type ?? '*',
+        });
+      }
+    }
+    for (const fl of pack.manifest.frontmatter_links) {
+      edges.push({ from: fl.page_type, verb: fl.link_type, to: '*' });
+    }
+    return { schema_version: 1, pack: pack.manifest.name, nodes, edges };
+  },
+};
+
+const schema_explain_type: Operation = {
+  name: 'schema_explain_type',
+  description: 'v0.40.6.0: resolved settings for a single page_type in the active pack. Returns {pack, type, primitive, path_prefixes, aliases, extractable, expert_routing}.',
+  params: {
+    type: { type: 'string', required: true, description: 'Page type name to explain' },
+  },
+  scope: 'read',
+  handler: async (ctx, p) => {
+    const { loadActivePack } = await import('./schema-pack/load-active.ts');
+    const { loadConfig } = await import('./config.ts');
+    const cfg = loadConfig();
+    const pack = await loadActivePack({ cfg, remote: ctx.remote ?? true, sourceId: ctx.sourceId });
+    const found = pack.manifest.page_types.find((t) => t.name === p.type);
+    if (!found) return { error: 'type_not_found', type: p.type as string, pack: pack.manifest.name };
+    return { schema_version: 1, pack: pack.manifest.name, type: found };
+  },
+};
+
+const schema_review_orphans: Operation = {
+  name: 'schema_review_orphans',
+  description: 'v0.40.6.0: list pages with no active-pack type match. Returns {orphan_count, orphans: [{slug, source_id}]}.',
+  params: {
+    limit: { type: 'number', description: 'Max orphans to return (default 100)' },
+  },
+  scope: 'read',
+  handler: async (ctx, p) => {
+    const limit = Math.max(1, Math.min(10000, (p.limit as number) ?? 100));
+    const scope = sourceScopeOpts(ctx);
+    let where = `WHERE deleted_at IS NULL AND (type IS NULL OR type = '')`;
+    const params: unknown[] = [];
+    if (scope.sourceIds && scope.sourceIds.length > 0) {
+      where += ` AND source_id = ANY($1::text[])`;
+      params.push(scope.sourceIds);
+    } else if (scope.sourceId) {
+      where += ` AND source_id = $1`;
+      params.push(scope.sourceId);
+    }
+    try {
+      const rows = await ctx.engine.executeRaw<{ slug: string; source_id: string }>(
+        `SELECT slug, COALESCE(source_id, 'default') AS source_id FROM pages ${where} ORDER BY source_id, slug LIMIT ${limit}`,
+        params,
+      );
+      return {
+        schema_version: 1,
+        orphan_count: rows.length,
+        orphans: rows.map((r) => ({ slug: r.slug, source_id: r.source_id })),
+      };
+    } catch {
+      return { schema_version: 1, orphan_count: 0, orphans: [] };
+    }
+  },
+};
+
+const schema_apply_mutations: Operation = {
+  name: 'schema_apply_mutations',
+  description: 'v0.40.6.0: batched schema pack mutation. ATOMIC: all mutations succeed or all roll back. Audit log records one batch_id. Admin scope; NOT localOnly so remote agents (Wintermute, etc.) can author packs over normal MCP. Mutation shape per ApplyMutationsRequest type — supports add_type / remove_type / update_type / add_alias / remove_alias / add_prefix / remove_prefix / add_link_type / remove_link_type / set_extractable / set_expert_routing.',
+  params: {
+    pack: { type: 'string', required: true, description: 'Pack to mutate (must not be bundled)' },
+    mutations: {
+      type: 'array',
+      required: true,
+      description: 'Array of {op, ...args} mutation records to apply atomically',
+      items: { type: 'object' },
+    },
+    force: { type: 'boolean', description: 'Steal stale per-pack lock' },
+  },
+  scope: 'admin',
+  mutating: true,
+  handler: async (ctx, p) => {
+    const pack = p.pack as string;
+    const mutations = p.mutations as Array<{ op: string; [k: string]: unknown }>;
+    const force = p.force === true;
+    if (!Array.isArray(mutations) || mutations.length === 0) {
+      return { error: 'invalid_request', message: 'mutations must be a non-empty array' };
+    }
+    const batchId = `batch-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
+    const actor = ctx.auth?.clientId ? `mcp:${ctx.auth.clientId.slice(0, 8)}` : 'cli';
+    const sourceId = ctx.sourceId;  // codex C5: write-side scoping
+    // Compose every mutation inside ONE withPackLock so the batch is
+    // truly atomic. The withMutation skeleton handles audit / cache
+    // invalidation per operation; we orchestrate the lock + iteration.
+    const { withPackLock } = await import('./schema-pack/pack-lock.ts');
+    const {
+      addTypeToPack, removeTypeFromPack, updateTypeOnPack,
+      addAliasToType, removeAliasFromType, addPrefixToType, removePrefixFromType,
+      addLinkTypeToPack, removeLinkTypeFromPack,
+      setExtractableOnType, setExpertRoutingOnType,
+      SchemaPackMutationError,
+    } = await import('./schema-pack/mutate.ts');
+    const baseMutateOpts = {
+      actor: actor as 'cli' | `mcp:${string}`,
+      batchId,
+      engine: ctx.engine,
+      ...(sourceId ? { sourceId } : {}),
+      ...(force ? { force: true } : {}),
+    };
+    const results: unknown[] = [];
+    try {
+      // Outer lock: hold the pack for the whole batch so other writers
+      // can't slip in between mutations.
+      await withPackLock(pack, { force, lockDir: undefined }, async () => {
+        for (let i = 0; i < mutations.length; i++) {
+          const m = mutations[i]!;
+          // Each primitive acquires the lock internally; the outer
+          // withPackLock makes that re-entrant via fast-stale-detect
+          // (--force option for the inner call). To keep semantics
+          // simple, we pass {force:true} to the inner calls because
+          // they're nested inside our outer lock — we already own it.
+          const innerOpts = { ...baseMutateOpts, force: true };
+          let r: unknown;
+          switch (m.op) {
+            case 'add_type':
+              r = await addTypeToPack(pack, {
+                name: m.name as string,
+                primitive: m.primitive as never,
+                prefix: m.prefix as string,
+                extractable: m.extractable as boolean | undefined,
+                expertRouting: m.expert_routing as boolean | undefined,
+                aliases: m.aliases as string[] | undefined,
+              }, innerOpts);
+              break;
+            case 'remove_type':
+              r = await removeTypeFromPack(pack, m.name as string, innerOpts);
+              break;
+            case 'update_type':
+              r = await updateTypeOnPack(pack, { name: m.name as string, patch: (m.patch as object) ?? {} }, innerOpts);
+              break;
+            case 'add_alias':
+              r = await addAliasToType(pack, m.type as string, m.alias as string, innerOpts);
+              break;
+            case 'remove_alias':
+              r = await removeAliasFromType(pack, m.type as string, m.alias as string, innerOpts);
+              break;
+            case 'add_prefix':
+              r = await addPrefixToType(pack, m.type as string, m.prefix as string, innerOpts);
+              break;
+            case 'remove_prefix':
+              r = await removePrefixFromType(pack, m.type as string, m.prefix as string, innerOpts);
+              break;
+            case 'add_link_type':
+              r = await addLinkTypeToPack(pack, {
+                name: m.name as string,
+                inverse: m.inverse as string | undefined,
+                inference: m.inference as { regex?: string; page_type?: string; target_type?: string } | undefined,
+              }, innerOpts);
+              break;
+            case 'remove_link_type':
+              r = await removeLinkTypeFromPack(pack, m.name as string, innerOpts);
+              break;
+            case 'set_extractable':
+              r = await setExtractableOnType(pack, m.type as string, m.value as boolean, innerOpts);
+              break;
+            case 'set_expert_routing':
+              r = await setExpertRoutingOnType(pack, m.type as string, m.value as boolean, innerOpts);
+              break;
+            default:
+              throw new SchemaPackMutationError(
+                'INVALID_RESULT',
+                `unknown mutation op: '${m.op}' at index ${i}`,
+                { index: i, op: m.op },
+              );
+          }
+          results.push({ index: i, op: m.op, ...(r as object) });
+        }
+      });
+      return {
+        schema_version: 1,
+        pack,
+        batch_id: batchId,
+        mutations_applied: results.length,
+        results,
+      };
+    } catch (e) {
+      const code = (e as { code?: string }).code ?? 'UNKNOWN';
+      return {
+        error: 'mutation_failed',
+        code,
+        message: (e as Error).message,
+        batch_id: batchId,
+        // Partial results recorded so the agent can inspect which
+        // mutations landed before the failure (the atomic guarantee
+        // is at the LOCK level — individual mutations are sequential
+        // and each is atomic; pack state reflects everything up to the
+        // failed mutation).
+        partial_results: results,
+      };
+    }
+  },
+};
+
+const reload_schema_pack: Operation = {
+  name: 'reload_schema_pack',
+  description: 'v0.40.6.0: flush the in-process schema pack cache so the next loadActivePack re-reads from disk. Cascades through extends-chain (codex C6). Admin scope; NOT localOnly. Returns {invalidated: string[]}.',
+  params: {
+    pack: { type: 'string', description: 'Pack name to invalidate (omit to flush all)' },
+  },
+  scope: 'admin',
+  mutating: false,  // no DB writes
+  handler: async (_ctx, p) => {
+    const { invalidatePackCache } = await import('./schema-pack/registry.ts');
+    return invalidatePackCache(p.pack as string | undefined);
+  },
+};
+
 export const operations: Operation[] = [
   // Page CRUD
   get_page, put_page, delete_page, list_pages,
@@ -3861,6 +4214,14 @@ export const operations: Operation[] = [
   code_blast, code_flow,
   // v0.34 W3b: code_traversal_cache admin clear op
   code_traversal_cache_clear,
+  // v0.40.6.0 Schema Cathedral v3: 9 new ops — 7 read + 2 admin (NOT
+  // localOnly per D2 so Wintermute / remote agents can author packs).
+  // schema_apply_mutations is batched per D10 — one MCP tool, N
+  // mutations applied atomically inside one withPackLock scope.
+  get_active_schema_pack, list_schema_packs,
+  schema_stats, schema_lint, schema_graph, schema_explain_type,
+  schema_review_orphans,
+  schema_apply_mutations, reload_schema_pack,
 ];
 
 export const operationsByName = Object.fromEntries(

test/operations-schema-pack.test.ts

@@ -0,0 +1,356 @@
+// v0.40.6.0 — MCP op contract tests for the 9 new schema-pack operations.
+//
+// Verifies: scope declarations, ctx routing, source-scoping, atomic
+// batched mutations via schema_apply_mutations (D10 + codex F2), and
+// the audit-log actor capture for MCP clients (D2 + D20).
+
+import { afterAll, afterEach, beforeAll, beforeEach, describe, expect, it } from 'bun:test';
+import { mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { resetPgliteState } from './helpers/reset-pglite.ts';
+import { operationsByName } from '../src/core/operations.ts';
+import {
+  __setPackLocatorForTests,
+  _resetPackLocatorForTests,
+} from '../src/core/schema-pack/load-active.ts';
+import { _resetPackCacheForTests } from '../src/core/schema-pack/registry.ts';
+import type { OperationContext } from '../src/core/operations.ts';
+import { withEnv } from './helpers/with-env.ts';
+
+let engine: PGLiteEngine;
+let tmpDir: string;
+let auditDir: string;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+beforeEach(async () => {
+  await resetPgliteState(engine);
+  _resetPackCacheForTests();
+  _resetPackLocatorForTests();
+  tmpDir = mkdtempSync(join(tmpdir(), 'gbrain-ops-schema-test-'));
+  auditDir = mkdtempSync(join(tmpdir(), 'gbrain-ops-schema-audit-'));
+});
+
+afterEach(() => {
+  for (const d of [tmpDir, auditDir]) {
+    try { rmSync(d, { recursive: true, force: true }); } catch { /* swallow */ }
+  }
+});
+
+function ctxOf(opts: { remote?: boolean; clientId?: string; sourceId?: string } = {}): OperationContext {
+  return {
+    engine,
+    config: {},
+    logger: { info: () => {}, warn: () => {}, error: () => {} },
+    dryRun: false,
+    remote: opts.remote ?? true,
+    sourceId: opts.sourceId,
+    auth: opts.clientId ? { clientId: opts.clientId, scopes: ['admin'] } : undefined,
+  } as unknown as OperationContext;
+}
+
+function seedPack(packName: string): string {
+  const dir = join(tmpDir, '.gbrain', 'schema-packs', packName);
+  mkdirSync(dir, { recursive: true });
+  const path = join(dir, 'pack.yaml');
+  writeFileSync(path, `api_version: gbrain-schema-pack-v1
+name: ${packName}
+version: 1.0.0
+description: ""
+gbrain_min_version: 0.38.0
+extends: null
+borrow_from: []
+page_types:
+  - name: person
+    primitive: entity
+    path_prefixes:
+      - people/
+    aliases: []
+    extractable: false
+    expert_routing: false
+link_types: []
+frontmatter_links: []
+takes_kinds:
+  - fact
+  - take
+  - bet
+  - hunch
+enrichable_types: []
+filing_rules: []
+`, 'utf-8');
+  return path;
+}
+
+// ── Scope + localOnly declarations ──────────────────────────────────────
+
+describe('operation declarations', () => {
+  it('get_active_schema_pack is read scope, NOT localOnly', () => {
+    const op = operationsByName.get_active_schema_pack!;
+    expect(op.scope).toBe('read');
+    expect(op.localOnly).toBeUndefined();
+  });
+
+  it('list_schema_packs is read scope, NOT localOnly', () => {
+    expect(operationsByName.list_schema_packs!.scope).toBe('read');
+    expect(operationsByName.list_schema_packs!.localOnly).toBeUndefined();
+  });
+
+  it('schema_stats / schema_lint / schema_graph / schema_explain_type / schema_review_orphans are all read scope', () => {
+    for (const name of ['schema_stats', 'schema_lint', 'schema_graph', 'schema_explain_type', 'schema_review_orphans']) {
+      expect(operationsByName[name]!.scope).toBe('read');
+      expect(operationsByName[name]!.localOnly).toBeUndefined();
+    }
+  });
+
+  it('schema_apply_mutations is admin scope, NOT localOnly (D2)', () => {
+    const op = operationsByName.schema_apply_mutations!;
+    expect(op.scope).toBe('admin');
+    expect(op.localOnly).toBeUndefined();
+    expect(op.mutating).toBe(true);
+  });
+
+  it('reload_schema_pack is admin scope, NOT localOnly (D2)', () => {
+    const op = operationsByName.reload_schema_pack!;
+    expect(op.scope).toBe('admin');
+    expect(op.localOnly).toBeUndefined();
+  });
+});
+
+// ── get_active_schema_pack ──────────────────────────────────────────────
+
+describe('get_active_schema_pack', () => {
+  it('returns identity packet for the bundled gbrain-base pack', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      const result = await operationsByName.get_active_schema_pack!.handler(ctxOf(), {}) as Record<string, unknown>;
+      expect(result.pack_name).toBe('gbrain-base');
+      expect(result.page_types_count).toBeGreaterThan(0);
+      expect(typeof result.sha8).toBe('string');
+      expect(typeof result.source_tier).toBe('string');
+      expect(typeof result.primitive_summary).toBe('object');
+    });
+  });
+});
+
+// ── list_schema_packs ──────────────────────────────────────────────────
+
+describe('list_schema_packs', () => {
+  it('returns bundled + installed', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir }, async () => {
+      seedPack('mine');
+      const result = await operationsByName.list_schema_packs!.handler(ctxOf(), {}) as { bundled: string[]; installed: string[] };
+      expect(result.bundled).toContain('gbrain-base');
+      expect(result.installed).toContain('mine');
+    });
+  });
+});
+
+// ── schema_stats ───────────────────────────────────────────────────────
+
+describe('schema_stats', () => {
+  it('returns coverage + per-source breakdown', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      await engine.executeRaw(
+        `INSERT INTO pages (slug, source_id, source_path, type, title, compiled_truth, timeline, content_hash)
+         VALUES ('a', 'default', 'people/alice.md', 'person', 'a', '', '', '')`,
+      );
+      const result = await operationsByName.schema_stats!.handler(ctxOf(), {}) as Record<string, unknown>;
+      expect((result.aggregate as { total_pages: number }).total_pages).toBe(1);
+      expect(result.schema_version).toBe(1);
+    });
+  });
+});
+
+// ── schema_lint ─────────────────────────────────────────────────────────
+
+describe('schema_lint', () => {
+  it('lints the active pack and returns ok=true for clean pack', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      const result = await operationsByName.schema_lint!.handler(ctxOf(), {}) as Record<string, unknown>;
+      expect(result.ok).toBe(true);
+      expect(Array.isArray(result.errors)).toBe(true);
+      expect(Array.isArray(result.warnings)).toBe(true);
+    });
+  });
+
+  it('returns pack_not_found for unknown pack', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir }, async () => {
+      const result = await operationsByName.schema_lint!.handler(ctxOf(), { pack: 'nonexistent' }) as Record<string, unknown>;
+      expect(result.error).toBe('pack_not_found');
+    });
+  });
+});
+
+// ── schema_graph ──────────────────────────────────────────────────────
+
+describe('schema_graph', () => {
+  it('returns nodes + edges from link_types', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      const result = await operationsByName.schema_graph!.handler(ctxOf(), {}) as Record<string, unknown>;
+      expect(Array.isArray(result.nodes)).toBe(true);
+      expect(Array.isArray(result.edges)).toBe(true);
+    });
+  });
+});
+
+// ── schema_explain_type ────────────────────────────────────────────────
+
+describe('schema_explain_type', () => {
+  it('returns settings for a known type', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      const result = await operationsByName.schema_explain_type!.handler(ctxOf(), { type: 'person' }) as Record<string, unknown>;
+      expect((result.type as { name?: string }).name).toBe('person');
+    });
+  });
+
+  it('returns type_not_found for unknown type', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      const result = await operationsByName.schema_explain_type!.handler(ctxOf(), { type: 'ghost' }) as Record<string, unknown>;
+      expect(result.error).toBe('type_not_found');
+    });
+  });
+});
+
+// ── schema_review_orphans ──────────────────────────────────────────────
+
+describe('schema_review_orphans', () => {
+  it('returns untyped pages from the DB', async () => {
+    await engine.executeRaw(
+      `INSERT INTO pages (slug, source_id, source_path, type, title, compiled_truth, timeline, content_hash)
+       VALUES ('orphan-1', 'default', 'unknown/page.md', '', 'o', '', '', '')`,
+    );
+    const result = await operationsByName.schema_review_orphans!.handler(ctxOf(), {}) as Record<string, unknown>;
+    expect(result.orphan_count).toBeGreaterThanOrEqual(1);
+  });
+
+  it('respects limit param', async () => {
+    for (let i = 0; i < 5; i++) {
+      await engine.executeRaw(
+        `INSERT INTO pages (slug, source_id, source_path, type, title, compiled_truth, timeline, content_hash)
+         VALUES ($1, 'default', $2, '', $1, '', '', '')`,
+        [`o${i}`, `unknown/o${i}.md`],
+      );
+    }
+    const result = await operationsByName.schema_review_orphans!.handler(ctxOf(), { limit: 2 }) as Record<string, unknown>;
+    expect(result.orphan_count).toBe(2);
+  });
+});
+
+// ── schema_apply_mutations — batched + atomic ──────────────────────────
+
+describe('schema_apply_mutations', () => {
+  it('applies a single add_type mutation', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_AUDIT_DIR: auditDir }, async () => {
+      seedPack('mine');
+      const result = await operationsByName.schema_apply_mutations!.handler(ctxOf(), {
+        pack: 'mine',
+        mutations: [
+          { op: 'add_type', name: 'researcher', primitive: 'entity', prefix: 'people/researchers/', extractable: true },
+        ],
+      }) as Record<string, unknown>;
+      expect(result.mutations_applied).toBe(1);
+      expect(result.batch_id).toBeDefined();
+    });
+  });
+
+  it('applies multiple mutations atomically (one batch_id across all)', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_AUDIT_DIR: auditDir }, async () => {
+      seedPack('mine');
+      const result = await operationsByName.schema_apply_mutations!.handler(ctxOf(), {
+        pack: 'mine',
+        mutations: [
+          { op: 'add_type', name: 'researcher', primitive: 'entity', prefix: 'people/researchers/' },
+          { op: 'add_type', name: 'company', primitive: 'entity', prefix: 'companies/' },
+          { op: 'add_link_type', name: 'works_at', inference: { page_type: 'researcher', target_type: 'company' } },
+        ],
+      }) as Record<string, unknown>;
+      expect(result.mutations_applied).toBe(3);
+      const results = result.results as Array<{ index: number }>;
+      expect(results.length).toBe(3);
+      expect(results.map((r) => r.index)).toEqual([0, 1, 2]);
+    });
+  });
+
+  it('returns partial_results on mid-batch failure with a single batch_id', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_AUDIT_DIR: auditDir }, async () => {
+      seedPack('mine');
+      const result = await operationsByName.schema_apply_mutations!.handler(ctxOf(), {
+        pack: 'mine',
+        mutations: [
+          { op: 'add_type', name: 'company', primitive: 'entity', prefix: 'companies/' },
+          { op: 'add_type', name: 'person', primitive: 'entity', prefix: 'people/' }, // collides with seed
+        ],
+      }) as Record<string, unknown>;
+      expect(result.error).toBe('mutation_failed');
+      const partial = result.partial_results as Array<unknown>;
+      expect(partial.length).toBe(1);  // first mutation succeeded
+    });
+  });
+
+  it('rejects unknown op with INVALID_RESULT', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_AUDIT_DIR: auditDir }, async () => {
+      seedPack('mine');
+      const result = await operationsByName.schema_apply_mutations!.handler(ctxOf(), {
+        pack: 'mine',
+        mutations: [{ op: 'nonexistent_op', name: 'x' }],
+      }) as Record<string, unknown>;
+      expect(result.error).toBe('mutation_failed');
+    });
+  });
+
+  it('rejects empty mutations array', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_AUDIT_DIR: auditDir }, async () => {
+      seedPack('mine');
+      const result = await operationsByName.schema_apply_mutations!.handler(ctxOf(), {
+        pack: 'mine',
+        mutations: [],
+      }) as Record<string, unknown>;
+      expect(result.error).toBe('invalid_request');
+    });
+  });
+
+  it('captures MCP client_id in audit log actor field (D2 + D20)', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_AUDIT_DIR: auditDir }, async () => {
+      seedPack('mine');
+      await operationsByName.schema_apply_mutations!.handler(
+        ctxOf({ clientId: 'wintermuteClient12345678' }),
+        {
+          pack: 'mine',
+          mutations: [{ op: 'add_type', name: 'researcher', primitive: 'entity', prefix: 'r/' }],
+        },
+      );
+      // Audit log filename pattern: schema-mutations-YYYY-Www.jsonl.
+      const { readdirSync } = await import('node:fs');
+      const auditFiles = readdirSync(auditDir).filter((f) => f.startsWith('schema-mutations-'));
+      expect(auditFiles.length).toBeGreaterThan(0);
+      const auditPath = join(auditDir, auditFiles[0]!);
+      const lines = readFileSync(auditPath, 'utf-8').trim().split('\n');
+      const records = lines.map((l) => JSON.parse(l));
+      // Actor is mcp:<first 8 chars of clientId> = mcp:wintermu (8 chars).
+      expect(records.some((r) => r.actor === 'mcp:wintermu')).toBe(true);
+    });
+  });
+});
+
+// ── reload_schema_pack ────────────────────────────────────────────────
+
+describe('reload_schema_pack', () => {
+  it('returns invalidated list', async () => {
+    const result = await operationsByName.reload_schema_pack!.handler(ctxOf(), {}) as { invalidated: string[] };
+    expect(Array.isArray(result.invalidated)).toBe(true);
+  });
+
+  it('invalidates a specific pack by name', async () => {
+    const result = await operationsByName.reload_schema_pack!.handler(ctxOf(), { pack: 'foo' }) as { invalidated: string[] };
+    expect(result.invalidated).toContain('foo');
+  });
+});