feat: add the minimal operational module lifecycle

Ekklesia had no notion of a module being on or off: the accepted module set
was exactly "whatever discovery found on disk", and `ModuleLifecycleStage`
named nine states nothing produced or consumed. This replaces that vocabulary
with two axes that real code produces — persistent, administrator-owned
configuration (`enabled`/`disabled`) and per-boot runtime observation
(`running`/`disabled`/`blocked`) — and wires them through startup.

- One Core table (`ekklesia_core_module_state`, migration 0004) holding only
  `module_id` and `enabled`. A module with no record is enabled by default, so
  deploying a module is still sufficient to run it and discovery never needs an
  initialization write. A record for an undeployed module is retained and
  ignored, so redeploying restores the decision.
- `resolveModuleEligibility` is pure: a disabled module transitively blocks
  every module that *requires* it (module and capability edges alike) with a
  structured reason naming the provider; optional dependencies never block; and
  a missing, incompatible, or cyclic dependency stays discovery's concern.
- `startApi` starts only the eligible set and builds the UI publication
  registry from that same list, so routes, artifacts, browser inventory, and
  Dashboard navigation all follow one authoritative set. A disabled module is
  never imported, so there is no per-request enablement check anywhere.
- Startup stays all-or-nothing, deliberately; there is consequently no `failed`
  runtime state. `pnpm modules:enable`/`modules:disable` is the out-of-band
  recovery path for a module that breaks startup.
- Changes take effect at the next start, and the read model reports
  configuration, runtime, and `restartRequired` separately rather than claiming
  a module stopped when it has not.
- Migration participation and permission composition still span the deployed
  and discovered inventories respectively, unchanged.
- New restricted platform permission `core.modules.lifecycle.manage` gates both
  reading and changing enablement, at a sibling prefix (`/api/v1/module-lifecycle`)
  that cannot collide with the module route namespace.
- `pnpm doctor` gains a `modules.lifecycle` check so "why is this module
  unavailable?" is answerable without reading logs.

See ADR 0028.

Co-Authored-By: Claude Opus 5 <[email protected]>

apps/api/tests/lifecycle.test.ts

@@ -48,6 +48,21 @@ function validConfig() {
   );
 }
 
+/**
+ * The one query behavior every fake pool in this file needs: startup reads the stored module
+ * enablement configuration (`ModuleLifecycleStore.readConfiguration`) before it imports any module
+ * entrypoint, and an installation that has never disabled anything genuinely has zero rows. Returning
+ * an empty result set is therefore the accurate stand-in for a real, migrated, unconfigured database
+ * — not a way to skip the read. The tests that care about a *specific* configuration drive the real
+ * resolver directly instead (`core/tests/module-lifecycle.test.ts`) or supply real rows through the
+ * real store (`core/tests/module-lifecycle-store.integration.ts`).
+ */
+function emptyQuery() {
+  return vi
+    .fn()
+    .mockResolvedValue({ command: "SELECT", fields: [], oid: 0, rowCount: 0, rows: [] });
+}
+
 const temporaryDirectories: string[] = [];
 
 async function createTemporaryModulesDirectory(): Promise<string> {
@@ -359,7 +374,7 @@ describe("Ekklesia API shutdown lifecycle", () => {
   it("makes every concurrent shutdown caller await the exact same server-close and pool-close, each exactly once", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     const { server } = mockSuccessfulServe();
@@ -375,7 +390,7 @@ describe("Ekklesia API shutdown lifecycle", () => {
   it("constructs exactly one physical PostgreSQL pool for both the identity and authorization views, and closes only that one pool on shutdown", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     mockSuccessfulServe();
@@ -395,7 +410,7 @@ describe("Ekklesia API shutdown lifecycle", () => {
   it("keeps shutdown idempotent for calls made after the first has already resolved", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     const { server } = mockSuccessfulServe();
@@ -411,7 +426,7 @@ describe("Ekklesia API shutdown lifecycle", () => {
   it("closes an already-created database pool when identity construction fails during startup", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockImplementation(() => {
       throw new Error("postgresql://admin:[email protected]/x");
@@ -429,7 +444,7 @@ describe("Ekklesia API shutdown lifecycle", () => {
   it("refuses a production configuration that enables public signup before any pool, Better Auth instance, module runtime, or server exists", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     mockSuccessfulServe();
@@ -467,7 +482,7 @@ describe("Ekklesia API shutdown lifecycle", () => {
   it("refuses an unsafe production database transport before any pool, Better Auth instance, module runtime, or server exists", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     mockSuccessfulServe();
@@ -520,7 +535,7 @@ describe("Ekklesia API shutdown lifecycle", () => {
   it("closes an already-created database pool when the server fails to bind its listen address", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     mockFailingServe(new Error("EADDRINUSE"));
@@ -584,7 +599,7 @@ describe("Ekklesia API Node server timeouts", () => {
   it("configures finite, typed header/request/keep-alive timeouts on the underlying Node server", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     mockSuccessfulServe();
@@ -621,7 +636,7 @@ describe("Ekklesia API Node server timeouts", () => {
   it("allows a test-only override to narrow the timeouts without changing the production defaults", async () => {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     mockSuccessfulServe();
@@ -673,7 +688,7 @@ describe("Ekklesia API Node server timeouts", () => {
   async function startAndCaptureClientErrorHandler() {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     const { clientErrorHandler } = mockSuccessfulServe();
@@ -891,7 +906,7 @@ describe("Ekklesia API module permission composition at startup", () => {
     const modulesDirectory = await createTemporaryModulesDirectory();
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     mockSuccessfulServe();
@@ -933,7 +948,7 @@ describe("Ekklesia API module runtime startup and shutdown", () => {
   function mockPoolAndAuth(): { poolEnd: ReturnType<typeof vi.fn> } {
     const poolEnd = vi.fn().mockResolvedValue(undefined);
     poolConstructor.mockImplementation(function fakePool() {
-      return { end: poolEnd, on: vi.fn() };
+      return { end: poolEnd, on: vi.fn(), query: emptyQuery() };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });
     return { poolEnd };
@@ -1131,6 +1146,7 @@ describe("Ekklesia API module runtime startup and shutdown", () => {
           recorder.events.push("pool:end");
         }),
         on: vi.fn(),
+        query: emptyQuery(),
       };
     });
     betterAuthMock.mockReturnValue({ api: { getSession: vi.fn() }, handler: vi.fn() });