feat: integrate module authorization

Wires composePlatformPermissionRegistry into apps/api's production
startup: startApi() discovers every installed module, composes the one
immutable platform permission registry (Core's own declarations plus
every module's), and only then constructs the shared PostgreSQL pool,
Better Auth, and the HTTP server. A discovery or composition failure —
an invalid manifest, a reserved core.* namespace claim, or a duplicate
declaration — propagates before anything exists to close; there is no
Core-only registry fallback. apps/api/src/platform-permissions.ts
resolves the repository root from its own file location, never
process.cwd(), so package-scoped test runs discover the right modules/
directory.

createApiApp/createGrantsRoutes now require the composed registry as
an injected authorization option, replacing the previous hard-coded
CORE_PERMISSION_REGISTRY; requirePermission continues to work
identically for Core-owned and module-owned permissions, since it has
no concept of the distinction.

Extends pnpm doctor with a modules.permissions check (reusing the
already-discovered module list, distinguishing reserved-namespace from
generic-duplicate failures, never re-discovering modules) and pnpm
modules:validate to compose the same registry before a module is
considered installable.

Adds focused coverage: startup-ordering and failure-isolation tests in
apps/api/tests/lifecycle.test.ts, module-owned-declaration enforcement
tests in apps/api/tests/authorization-middleware.test.ts, Doctor
composition tests in core/tests/doctor.test.ts, and a live PostgreSQL
end-to-end scenario proving a real installed module's permission is
discoverable, grantable, and deniable once the module is absent again
after a restart, without ever executing its server entrypoint.

apps/api/src/server.ts

@@ -5,11 +5,13 @@ import {
   createAuthorizationStore,
 } from "@ekklesia/core/authorization";
 import { createIdentityRuntime, type IdentityRateLimitOverride } from "@ekklesia/core/identity";
+import type { DiscoveredModule } from "@ekklesia/core/modules";
 import { serve, type ServerType } from "@hono/node-server";
 import type { Hono } from "hono";
 import { createApiApp } from "./app.js";
 import { type ApiRuntimeConfig, createApiRuntimeConfig } from "./config.js";
 import { type ApiDatabaseHandle, createApiDatabase } from "./database.js";
+import { composeStartupPermissionRegistry } from "./platform-permissions.js";
 
 const connectionTimeoutMs = 10_000;
 const operationTimeoutMs = 10_000;
@@ -24,6 +26,13 @@ export interface StartApiOptions {
   /** Test-only escape hatch: never set by the executable entry point. See
    * `IdentityRateLimitOverride` for why production must leave this unset. */
   readonly rateLimitOverride?: IdentityRateLimitOverride;
+  /** Test-only escape hatch: overrides the directory permission-composition module discovery
+   * scans. Never set by the executable entry point. See `composeStartupPermissionRegistry`. */
+  readonly modulesDirectoryOverride?: string;
+  /** Test-only escape hatch: supplies an already-discovered module list directly to permission
+   * composition, skipping filesystem discovery entirely. Never set by the executable entry
+   * point. See `composeStartupPermissionRegistry`. */
+  readonly discoveredModulesOverride?: readonly DiscoveredModule[];
 }
 
 async function safeCloseDatabase(handle: ApiDatabaseHandle): Promise<void> {
@@ -54,18 +63,33 @@ function bindServer(app: Hono, host: string, port: number): Promise<ServerType>
 }
 
 /**
- * Explicit runtime composition: constructs the one shared PostgreSQL pool (identity and
- * authorization each get a typed Drizzle view over it — see `./database.js`), the Core identity
- * runtime, the Core authorization store and evaluator, and the Hono application, then starts the
- * Node HTTP server. Returns a handle with an idempotent `shutdown()` so both the executable entry
- * point and tests can stop the server and close the shared pool deterministically. Never applies
- * migrations or generates schema — the database must already be migrated through
- * `pnpm migrations:apply`.
+ * Explicit runtime composition, in a fixed order: discover every installed module's manifest and
+ * compose the one immutable platform permission registry from Core's own declarations plus every
+ * module's (`./platform-permissions.js`); only then construct the one shared PostgreSQL pool
+ * (identity and authorization each get a typed Drizzle view over it — see `./database.js`), the
+ * Core identity runtime, the Core authorization store and evaluator, and the Hono application;
+ * finally start the Node HTTP server. Permission composition happens before any pool, Better
+ * Auth instance, or HTTP server exists, so a discovery or composition failure — an invalid
+ * manifest, a dependency-graph problem, a module claiming the reserved `core.*` permission
+ * namespace, or a duplicate permission declaration — leaves nothing to close: it propagates
+ * directly, and startup never falls back to a Core-only registry. Returns a handle with an
+ * idempotent `shutdown()` so both the executable entry point and tests can stop the server and
+ * close the shared pool deterministically. Never applies migrations or generates schema — the
+ * database must already be migrated through `pnpm migrations:apply`.
  */
 export async function startApi(
   config: ApiRuntimeConfig,
   options: StartApiOptions = {},
 ): Promise<RunningApi> {
+  const permissionRegistry = await composeStartupPermissionRegistry({
+    ...(options.modulesDirectoryOverride === undefined
+      ? {}
+      : { modulesDirectoryOverride: options.modulesDirectoryOverride }),
+    ...(options.discoveredModulesOverride === undefined
+      ? {}
+      : { discoveredModulesOverride: options.discoveredModulesOverride }),
+  });
+
   const databaseHandle = createApiDatabase(config.databaseUrl, {
     connectionTimeoutMs,
     operationTimeoutMs,
@@ -91,7 +115,7 @@ export async function startApi(
   });
 
   const app = createApiApp({
-    authorization: { evaluator, store: authorizationStore },
+    authorization: { evaluator, registry: permissionRegistry, store: authorizationStore },
     runtime,
     trustedOrigins: config.identity.trustedOrigins,
   });