feat: one generic image, with installed modules in installation-owned storage (ADR 0048)

The production image now contains zero feature modules and is the same for every
installation. Installed modules live in module storage that one Core resolver
selects from EKKLESIA_MODULES_DIR: the checkout's modules/ when unset, an
absolute path that must exist when set (/var/lib/ekklesia/modules in the image).
A relative, blank, missing, or unreadable configured directory fails closed with
a sanitized error that never contains the value.

- Host configuration reads EKKLESIA_MODULES_DIR. The API, migration plan, apply
  and validate, module validation, module enablement, and Doctor all resolve it
  the same way; the test-only API override still takes precedence.
- Doctor receives Core's migrations directory explicitly instead of deriving it
  from the modules directory's parent.
- The migration runner retains and reports the applied history of a module that
  is not installed, and plans and applies Core's and present modules' migrations
  around it. Core's history and every installed module's history stay strict: a
  missing or changed applied migration, or a downgrade, still fails. No down
  migrations, no data deletion.
- deploy/Dockerfile copies no module and installs nothing for the module
  template; .dockerignore excludes modules/ and the build refuses a context that
  contains it; the runtime has an empty root-owned /var/lib/ekklesia/modules and
  sets EKKLESIA_MODULES_DIR.
- deploy/compose.yaml bind-mounts EKKLESIA_MODULES_HOST_DIR read-only into api
  and migrate, with create_host_path disabled.
- scripts/check-image.sh proves the image holds no modules and that a populated
  modules/ directory leaves its runtime file system identical; CI runs it.
- The split deploy smoke now uses the same generic image: it boots with no
  modules, installs a self-contained test module packaged from the template
  (test-only), migrates and restarts, removes it (Core runs, planning reports the
  retained history, data survives), and restores it with its data.

Docs: deploy README (module storage, install/update/remove/restore, the runtime
modules target), .env.example, API configuration, module development guide,
testing, workflow, security, and the architecture overview.

Co-Authored-By: Claude Opus 5.5 <[email protected]>

core/tests/doctor-host-configuration.test.ts

@@ -8,10 +8,11 @@ import {
   diagnoseEkklesia,
   formatDoctorReport,
 } from "../src/diagnostics/index.js";
-import type {
-  DiscoveredModule,
-  ModuleMigrationAggregate,
-  ModuleSchemaAggregate,
+import {
+  type DiscoveredModule,
+  discoverModules,
+  type ModuleMigrationAggregate,
+  type ModuleSchemaAggregate,
 } from "../src/modules/index.js";
 
 /**
@@ -34,8 +35,8 @@ const moduleSecret = "module-secret-material";
 
 const metadata = Object.freeze({
   moduleSdkVersion: "0.1.0",
-  modulesDirectory: "/not-rendered/modules",
   platformVersion: "0.1.0",
+  repositoryRoot: "/not-rendered",
   runtimeRange: ">=24.11.0 <25",
   runtimeVersion: "24.15.0",
 });
@@ -454,3 +455,33 @@ describe("Doctor host-configuration parity — sanitization", () => {
     expect(JSON.stringify(report)).not.toContain("S3_ACCESS_KEY");
   });
 });
+
+describe("Doctor reads the modules directory from the same host configuration (ADR 0048)", () => {
+  it("uses the repository's own modules directory when EKKLESIA_MODULES_DIR is unset", () => {
+    const doctorOptions = createDoctorOptions(environment(), metadata);
+    expect(doctorOptions.moduleDiscovery.modulesDirectory).toBe("/not-rendered/modules");
+    expect(doctorOptions.moduleDiscovery.modulesDirectoryRequired).toBe(false);
+    expect(doctorOptions.coreMigrationsDirectory).toBe("/not-rendered/core/drizzle");
+  });
+
+  it("uses a configured directory, and still finds Core's migrations under the platform", () => {
+    const doctorOptions = createDoctorOptions(
+      environment({ EKKLESIA_MODULES_DIR: "/var/lib/ekklesia/modules" }),
+      metadata,
+    );
+    expect(doctorOptions.moduleDiscovery.modulesDirectory).toBe("/var/lib/ekklesia/modules");
+    expect(doctorOptions.moduleDiscovery.modulesDirectoryRequired).toBe(true);
+    expect(doctorOptions.coreMigrationsDirectory).toBe("/not-rendered/core/drizzle");
+  });
+
+  it("hands an unusable value to discovery to report, rather than throwing before a report exists", async () => {
+    const doctorOptions = createDoctorOptions(
+      environment({ EKKLESIA_MODULES_DIR: "relative/private-mount-91aa" }),
+      metadata,
+    );
+    expect(doctorOptions.moduleDiscovery.modulesDirectoryRequired).toBe(true);
+    const report = await diagnoseEkklesia(doctorOptions, dependencies({ discoverModules }));
+    expect(report.checks.find((entry) => entry.id === "modules.discovery")?.status).toBe("failure");
+    expect(JSON.stringify(report)).not.toContain("private-mount-91aa");
+  });
+});

core/tests/doctor-report.test.ts

@@ -68,6 +68,7 @@ describe("Ekklesia Doctor terminal report", () => {
   it("renders the real zero-module and no-database shape exactly", async () => {
     const report = await diagnoseEkklesia(
       {
+        coreMigrationsDirectory: "/not-rendered/core/drizzle",
         moduleDiscovery: {
           moduleSdkVersion: "0.1.0",
           modulesDirectory: "/not-rendered/modules",
@@ -135,6 +136,7 @@ Result: READY WITH WARNINGS`);
   it("renders every check the report contains, so none can silently affect the result", async () => {
     const report = await diagnoseEkklesia(
       {
+        coreMigrationsDirectory: "/not-rendered/core/drizzle",
         moduleDiscovery: {
           moduleSdkVersion: "0.1.0",
           modulesDirectory: "/not-rendered/modules",
@@ -159,6 +161,7 @@ Result: READY WITH WARNINGS`);
   it("does not depend on NO_COLOR or terminal interactivity", async () => {
     const report = await diagnoseEkklesia(
       {
+        coreMigrationsDirectory: "/not-rendered/core/drizzle",
         moduleDiscovery: {
           moduleSdkVersion: "0.1.0",
           modulesDirectory: "/not-rendered/modules",
@@ -207,6 +210,7 @@ Result: READY WITH WARNINGS`);
     const report = await diagnoseEkklesia(
       {
         databaseUrl: "postgresql://another:[email protected]/db",
+        coreMigrationsDirectory: "/not-rendered/core/drizzle",
         moduleDiscovery: {
           moduleSdkVersion: "0.1.0",
           modulesDirectory: "/not-rendered/modules",

core/tests/doctor.test.ts

@@ -1,5 +1,9 @@
 import { type ModuleManifest, parsePermissionId } from "@ekklesia/contracts";
-import { describe, expect, it, vi } from "vitest";
+import { mkdtemp, rm } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import { afterEach, describe, expect, it, vi } from "vitest";
 import { createPermissionRegistry, PermissionRegistryError } from "../src/authorization/index.js";
 import {
   type DoctorCheck,
@@ -114,7 +118,10 @@ function emptyDatabase(): MigrationDatabase {
   });
 }
 
-function plan(entries: MigrationPlanResult["entries"] = []): MigrationPlanResult {
+function plan(
+  entries: MigrationPlanResult["entries"] = [],
+  retained: MigrationPlanResult["retained"] = [],
+): MigrationPlanResult {
   const appliedCount = entries.filter((entry) => entry.status === "applied").length;
   const approvalRequiredCount = entries.filter(
     (entry) => entry.status === "approval-blocked",
@@ -124,6 +131,7 @@ function plan(entries: MigrationPlanResult["entries"] = []): MigrationPlanResult
     approvalRequiredCount,
     entries: Object.freeze([...entries]),
     pendingCount: entries.length - appliedCount,
+    retained: Object.freeze([...retained]),
   });
 }
 
@@ -151,6 +159,7 @@ function dependencies(overrides: Partial<DoctorDependencies> = {}): DoctorDepend
 function options(databaseUrl?: string): DoctorOptions {
   return {
     ...(databaseUrl === undefined ? {} : { databaseUrl }),
+    coreMigrationsDirectory: "/not-rendered/core/drizzle",
     moduleDiscovery: {
       moduleSdkVersion: "0.1.0",
       modulesDirectory: "/not-rendered/modules",
@@ -1657,3 +1666,113 @@ describe("Doctor reports declared browser contributions", () => {
     ]);
   });
 });
+
+describe("Doctor with installation-owned module storage (ADR 0048)", () => {
+  const platformCoreMigrations = path.join(
+    path.dirname(fileURLToPath(import.meta.url)),
+    "..",
+    "drizzle",
+  );
+  const temporaryDirectories: string[] = [];
+
+  afterEach(async () => {
+    await Promise.all(
+      temporaryDirectories.splice(0).map((directory) => rm(directory, { recursive: true })),
+    );
+  });
+
+  it("finds Core's migrations where the platform is installed, not beside the modules", async () => {
+    // A modules directory far from the platform, as the image mounts /var/lib/ekklesia/modules. Its
+    // parent has no `core/drizzle`, so a Doctor that still derived Core's migrations from the
+    // modules directory would fail migration discovery here.
+    const external = await mkdtemp(path.join(tmpdir(), "ekklesia-external-modules-"));
+    temporaryDirectories.push(external);
+    const report = await diagnoseEkklesia({
+      coreMigrationsDirectory: platformCoreMigrations,
+      moduleDiscovery: {
+        moduleSdkVersion: "0.1.0",
+        modulesDirectory: external,
+        modulesDirectoryRequired: true,
+        platformVersion: "0.1.0",
+      },
+      runtimeRange: ">=24.11.0 <25",
+      runtimeVersion: "24.15.0",
+    });
+
+    expect(check(report, "modules.discovery").status).toBe("pass");
+    const migrations = check(report, "migrations.discovery");
+    expect(migrations.status).toBe("pass");
+    expect(migrations.details.some((detail) => detail.startsWith("core:0000_"))).toBe(true);
+    expect(JSON.stringify(report)).not.toContain(external);
+  });
+
+  it("reports an unusable configured modules directory as a discovery failure, naming no path", async () => {
+    const report = await diagnoseEkklesia({
+      coreMigrationsDirectory: platformCoreMigrations,
+      moduleDiscovery: {
+        moduleSdkVersion: "0.1.0",
+        modulesDirectory: "relative/private-mount-3c9d",
+        modulesDirectoryRequired: true,
+        platformVersion: "0.1.0",
+      },
+      runtimeRange: ">=24.11.0 <25",
+      runtimeVersion: "24.15.0",
+    });
+
+    const discovery = check(report, "modules.discovery");
+    expect(discovery.status).toBe("failure");
+    expect(discovery.details).toEqual(["The configured modules directory is not usable."]);
+    expect(check(report, "migrations.discovery").status).toBe("skipped");
+    expect(JSON.stringify(report)).not.toContain("private-mount-3c9d");
+  });
+
+  it("reports a configured modules directory that does not exist, naming no path", async () => {
+    const parent = await mkdtemp(path.join(tmpdir(), "ekklesia-missing-modules-"));
+    temporaryDirectories.push(parent);
+    const report = await diagnoseEkklesia({
+      coreMigrationsDirectory: platformCoreMigrations,
+      moduleDiscovery: {
+        moduleSdkVersion: "0.1.0",
+        modulesDirectory: path.join(parent, "absent"),
+        modulesDirectoryRequired: true,
+        platformVersion: "0.1.0",
+      },
+      runtimeRange: ">=24.11.0 <25",
+      runtimeVersion: "24.15.0",
+    });
+
+    const discovery = check(report, "modules.discovery");
+    expect(discovery.status).toBe("failure");
+    expect(discovery.details).toEqual(["The configured modules directory could not be read."]);
+    expect(JSON.stringify(report)).not.toContain(parent);
+  });
+
+  it("reports an absent module's retained history without blocking readiness", async () => {
+    const report = await diagnoseEkklesia(
+      options("postgres://[email protected]/ekklesia"),
+      dependencies({
+        planMigrations: vi.fn(async () =>
+          plan(
+            [planEntry("core:0000_identity_core_tables", "a".repeat(64), "applied")],
+            [Object.freeze({ appliedCount: 2, moduleId: "calendar" })],
+          ),
+        ),
+      }),
+    );
+
+    const planCheck = check(report, "postgresql.plan");
+    expect(planCheck.status).toBe("pass");
+    expect(planCheck.details).toContain(
+      "retained · calendar · 2 applied migrations kept; the module is not installed",
+    );
+  });
+
+  it("passes Core's own migration directory to migration discovery", async () => {
+    const discoverMigrations = vi.fn(async () => migrationAggregate());
+    await diagnoseEkklesia(options(), dependencies({ discoverMigrations }));
+    expect(discoverMigrations).toHaveBeenCalledWith({
+      coreMigrationsDirectory: "/not-rendered/core/drizzle",
+      moduleDiscovery: options().moduleDiscovery,
+    });
+  });
+});

core/tests/host-configuration-boundaries.test.ts

@@ -68,6 +68,7 @@ const INTERPRETED_VARIABLES = Object.freeze([
   "EKKLESIA_IDENTITY_BASE_URL",
   "EKKLESIA_IDENTITY_SECRET",
   "EKKLESIA_IDENTITY_TRUSTED_ORIGINS",
+  "EKKLESIA_MODULES_DIR",
   "EKKLESIA_PUBLIC_SIGNUP_ENABLED",
   "EKKLESIA_SMTP_FROM_ADDRESS",
   "EKKLESIA_SMTP_FROM_NAME",

core/tests/host-configuration.test.ts

@@ -48,6 +48,19 @@ describe("host configuration loading", () => {
     expect(host.identity.secret).toBeUndefined();
   });
 
+  it("carries the configured modules directory verbatim, and nothing when it is unset", () => {
+    expect(loadHostConfiguration({}).modulesDirectory).toBeUndefined();
+    expect(
+      loadHostConfiguration({ EKKLESIA_MODULES_DIR: "/var/lib/ekklesia/modules" }).modulesDirectory,
+    ).toBe("/var/lib/ekklesia/modules");
+    // Validation is the resolver's job (ADR 0048). The loader neither repairs a relative or blank
+    // value nor treats a set-but-empty variable as unset, so the resolver can refuse it.
+    expect(
+      loadHostConfiguration({ EKKLESIA_MODULES_DIR: "relative/modules" }).modulesDirectory,
+    ).toBe("relative/modules");
+    expect(loadHostConfiguration({ EKKLESIA_MODULES_DIR: "" }).modulesDirectory).toBe("");
+  });
+
   it("carries every object-storage field the storage passes established", () => {
     const host = loadHostConfiguration(productionEnvironment);
 

core/tests/migration-report.test.ts

@@ -40,6 +40,7 @@ describe("migration command reports", () => {
         }),
       ]),
       pendingCount: 2,
+      retained: Object.freeze([]),
     });
 
     expect(formatMigrationPlanReport(plan)).toEqual([
@@ -64,6 +65,7 @@ describe("migration command reports", () => {
       ]),
       appliedCount: 1,
       noOp: false,
+      retained: Object.freeze([]),
     });
 
     expect(formatMigrationApplyReport(applied)).toEqual([
@@ -72,7 +74,12 @@ describe("migration command reports", () => {
     ]);
     expect(
       formatMigrationApplyReport(
-        Object.freeze({ applied: Object.freeze([]), appliedCount: 0, noOp: true }),
+        Object.freeze({
+          applied: Object.freeze([]),
+          appliedCount: 0,
+          noOp: true,
+          retained: Object.freeze([]),
+        }),
       ),
     ).toEqual(["Migration apply completed: database is already current (no changes)."]);
   });
@@ -85,6 +92,7 @@ describe("migration command reports", () => {
           approvalRequiredCount: 0,
           entries: Object.freeze([]),
           pendingCount: 0,
+          retained: Object.freeze([]),
         }),
       ),
     ).toEqual([
@@ -93,4 +101,62 @@ describe("migration command reports", () => {
       "Informational only: this plan is read-only and may become stale; apply revalidates history under the migration lock.",
     ]);
   });
+
+  it("reports an absent module's retained history without treating it as work (ADR 0048)", () => {
+    const retained = Object.freeze([
+      Object.freeze({ appliedCount: 1, moduleId: "calendar" }),
+      Object.freeze({ appliedCount: 3, moduleId: "signage" }),
+    ]);
+    const retainedLines = [
+      "- [retained] calendar: 1 applied migration kept; the module is not installed",
+      "- [retained] signage: 3 applied migrations kept; the module is not installed",
+    ];
+
+    expect(
+      formatMigrationPlanReport(
+        Object.freeze({
+          appliedCount: 0,
+          approvalRequiredCount: 0,
+          entries: Object.freeze([]),
+          pendingCount: 0,
+          retained,
+        }),
+      ),
+    ).toEqual([
+      "Migration plan (0 applied, 0 pending, 0 approval-blocked, 2 retained):",
+      "- No installed module migrations.",
+      ...retainedLines,
+      "Informational only: this plan is read-only and may become stale; apply revalidates history under the migration lock.",
+    ]);
+    expect(
+      formatMigrationApplyReport(
+        Object.freeze({ applied: Object.freeze([]), appliedCount: 0, noOp: true, retained }),
+      ),
+    ).toEqual([
+      "Migration apply completed: database is already current (no changes).",
+      ...retainedLines,
+    ]);
+    expect(
+      formatMigrationApplyReport(
+        Object.freeze({
+          applied: Object.freeze([
+            Object.freeze({
+              checksum: "e".repeat(64),
+              identity: "core:0007_later",
+              index: 7,
+              moduleId: "core",
+              tag: "0007_later",
+            }),
+          ]),
+          appliedCount: 1,
+          noOp: false,
+          retained,
+        }),
+      ),
+    ).toEqual([
+      "Migration apply completed (1 migration applied):",
+      `- core:0007_later sha256=${"e".repeat(64)}`,
+      ...retainedLines,
+    ]);
+  });
 });

core/tests/module-migration-runner.test.ts

@@ -13,6 +13,7 @@ import {
   type MigrationTransaction,
   planModuleMigrations,
 } from "../src/migrations/runner.js";
+import type { DiscoveredModule } from "../src/modules/discovery.js";
 import type {
   DiscoveredModuleMigration,
   ModuleMigrationAggregate,
@@ -323,6 +324,7 @@ describe("module migration planning", () => {
         },
       ],
       pendingCount: 1,
+      retained: [],
     });
     expect(database.events).toEqual(["session:open", "history:read", "session:close"]);
     expect(database.historyTableExists).toBe(false);
@@ -344,10 +346,11 @@ describe("module migration planning", () => {
       approvalRequiredCount: 0,
       entries: [],
       pendingCount: 0,
+      retained: [],
     });
     expect(Object.isFrozen(result)).toBe(true);
     expect(Object.isFrozen(result.entries)).toBe(true);
-    expect(applyResult).toEqual({ applied: [], appliedCount: 0, noOp: true });
+    expect(applyResult).toEqual({ applied: [], appliedCount: 0, noOp: true, retained: [] });
     expect(database.historyTableExists).toBe(false);
     expect(database.events).not.toContain("transaction:begin");
   });
@@ -548,6 +551,7 @@ describe("module migration apply", () => {
       ],
       appliedCount: 1,
       noOp: false,
+      retained: [],
     });
   });
 
@@ -580,7 +584,7 @@ describe("module migration apply", () => {
       database,
     });
 
-    expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true });
+    expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true, retained: [] });
     expect(Object.isFrozen(result)).toBe(true);
     expect(Object.isFrozen(result.applied)).toBe(true);
     expectNoPersistentMutation(database);
@@ -601,7 +605,7 @@ describe("module migration apply", () => {
       database,
     });
 
-    expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true });
+    expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true, retained: [] });
     expect(database.historyTableExists).toBe(false);
     expect(database.events).toEqual([
       "session:open",
@@ -980,3 +984,250 @@ describe("module migration failures and side effects", () => {
     expect(database.committedHistory).toEqual([]);
   });
 });
+
+/**
+ * Marks modules as present in the discovered inventory without giving them migrations, the way a
+ * real aggregate lists every discovered module whether or not it owns migration history. Only the
+ * manifest id is read by the runner.
+ */
+function withDiscovered(
+  inventory: ModuleMigrationAggregate,
+  ...moduleIds: readonly string[]
+): ModuleMigrationAggregate {
+  return Object.freeze({
+    ...inventory,
+    discoveredModules: Object.freeze(
+      moduleIds.map((id) => ({ manifest: { id } }) as unknown as DiscoveredModule),
+    ),
+  });
+}
+
+describe("retained history for absent modules (ADR 0048)", () => {
+  it("retains and reports an absent module's applied history without failing the plan", async () => {
+    const coreInitial = migration("core", 0);
+    const calendarInitial = migration("calendar", 0);
+    const calendarLater = migration("calendar", 1);
+    const history = [
+      historyRecord(coreInitial, 1),
+      historyRecord(calendarInitial, 2),
+      historyRecord(calendarLater, 3),
+    ];
+    const database = new FakeMigrationDatabase({ history });
+
+    const result = await planModuleMigrations({
+      aggregate: aggregate({ id: "core", migrations: [coreInitial] }),
+      database,
+    });
+
+    expect(result.appliedCount).toBe(1);
+    expect(result.pendingCount).toBe(0);
+    expect(result.entries.map((entry) => entry.identity)).toEqual([coreInitial.identity]);
+    expect(result.retained).toEqual([{ appliedCount: 2, moduleId: "calendar" }]);
+    expect(Object.isFrozen(result.retained)).toBe(true);
+    expect(Object.isFrozen(result.retained[0])).toBe(true);
+    expect(database.committedHistory).toEqual(history);
+    expectNoPersistentMutation(database);
+  });
+
+  it("applies a later Core migration while a module is absent, leaving its history intact", async () => {
+    const coreInitial = migration("core", 0);
+    const coreLater = migration("core", 1);
+    const calendarInitial = migration("calendar", 0);
+    const history = [historyRecord(coreInitial, 1), historyRecord(calendarInitial, 2)];
+    const database = new FakeMigrationDatabase({ history });
+
+    const result = await applyModuleMigrations({
+      aggregate: aggregate({ id: "core", migrations: [coreInitial, coreLater] }),
+      database,
+    });
+
+    expect(result.applied.map((applied) => applied.identity)).toEqual([coreLater.identity]);
+    expect(result.retained).toEqual([{ appliedCount: 1, moduleId: "calendar" }]);
+    expect(database.executedStatements).toEqual([coreLater.sql]);
+    expect(database.committedHistory.map((record) => record.identity)).toEqual([
+      coreInitial.identity,
+      calendarInitial.identity,
+      coreLater.identity,
+    ]);
+  });
+
+  it("applies a present module's migrations while another module is absent", async () => {
+    const peopleInitial = migration("people", 0);
+    const calendarInitial = migration("calendar", 0);
+    const database = new FakeMigrationDatabase({ history: [historyRecord(calendarInitial, 1)] });
+
+    const result = await applyModuleMigrations({
+      aggregate: aggregate({ id: "people", migrations: [peopleInitial] }),
+      database,
+    });
+
+    expect(result.applied.map((applied) => applied.identity)).toEqual([peopleInitial.identity]);
+    expect(result.retained).toEqual([{ appliedCount: 1, moduleId: "calendar" }]);
+  });
+
+  it("reports retained modules in a stable order with exact counts", async () => {
+    const zeta = [migration("zeta", 0), migration("zeta", 1), migration("zeta", 2)];
+    const alpha = migration("alpha", 0);
+    const database = new FakeMigrationDatabase({
+      history: [
+        historyRecord(zeta[0] as DiscoveredModuleMigration, 1),
+        historyRecord(alpha, 2),
+        historyRecord(zeta[1] as DiscoveredModuleMigration, 3),
+        historyRecord(zeta[2] as DiscoveredModuleMigration, 4),
+      ],
+    });
+
+    const result = await planModuleMigrations({ aggregate: aggregate(), database });
+
+    expect(result.retained).toEqual([
+      { appliedCount: 1, moduleId: "alpha" },
+      { appliedCount: 3, moduleId: "zeta" },
+    ]);
+  });
+
+  it("returns a module to strict validation: valid history plans cleanly and nothing is retained", async () => {
+    const initial = migration("people", 0);
+    const later = migration("people", 1);
+    const database = new FakeMigrationDatabase({ history: [historyRecord(initial, 1)] });
+
+    const result = await planModuleMigrations({
+      aggregate: aggregate({ id: "people", migrations: [initial, later] }),
+      database,
+    });
+
+    expect(result.retained).toEqual([]);
+    expect(result.entries.map((entry) => [entry.identity, entry.status])).toEqual([
+      [initial.identity, "applied"],
+      [later.identity, "pending"],
+    ]);
+  });
+
+  it("fails when a returning module no longer ships a previously applied migration", async () => {
+    const initial = migration("people", 0);
+    const later = migration("people", 1);
+    const database = new FakeMigrationDatabase({
+      history: [historyRecord(initial, 1), historyRecord(later, 2)],
+    });
+    const downgraded = aggregate({ id: "people", migrations: [initial] });
+
+    await captureRunnerError(
+      planModuleMigrations({ aggregate: downgraded, database }),
+      "MIGRATION_UNKNOWN_APPLIED",
+    );
+    await captureRunnerError(
+      applyModuleMigrations({ aggregate: downgraded, database }),
+      "MIGRATION_UNKNOWN_APPLIED",
+    );
+    expect(database.executedStatements).toEqual([]);
+  });
+
+  it("fails when a returning module's applied migration has different contents", async () => {
+    const initial = migration("people", 0);
+    const database = new FakeMigrationDatabase({ history: [historyRecord(initial, 1)] });
+    const edited = aggregate({
+      id: "people",
+      migrations: [migration("people", 0, { sql: "SELECT 'edited';\n" })],
+    });
+
+    const error = await captureRunnerError(
+      planModuleMigrations({ aggregate: edited, database }),
+      "MIGRATION_CHECKSUM_MISMATCH",
+    );
+    expect(error.migrationIdentity).toBe(initial.identity);
+  });
+
+  it("fails when a returning module's history is no longer a prefix of its journal", async () => {
+    const initial = migration("people", 0);
+    const later = migration("people", 1);
+    const database = new FakeMigrationDatabase({ history: [historyRecord(later, 1)] });
+
+    await captureRunnerError(
+      planModuleMigrations({
+        aggregate: aggregate({ id: "people", migrations: [initial, later] }),
+        database,
+      }),
+      "MIGRATION_HISTORY_INVALID",
+    );
+  });
+
+  it("keeps a present module that no longer ships any migrations strict", async () => {
+    const initial = migration("people", 0);
+    const database = new FakeMigrationDatabase({ history: [historyRecord(initial, 1)] });
+
+    await captureRunnerError(
+      planModuleMigrations({ aggregate: withDiscovered(aggregate(), "people"), database }),
+      "MIGRATION_UNKNOWN_APPLIED",
+    );
+  });
+
+  it("never treats Core's history as an absent module's", async () => {
+    const coreInitial = migration("core", 0);
+    const coreGhost = migration("core", 1);
+
+    // An inventory with no Core source at all: Core's rows are still strict, never retained.
+    await captureRunnerError(
+      planModuleMigrations({
+        aggregate: aggregate({ id: "people", migrations: [] }),
+        database: new FakeMigrationDatabase({ history: [historyRecord(coreInitial, 1)] }),
+      }),
+      "MIGRATION_UNKNOWN_APPLIED",
+    );
+    // A Core row missing from Core's own inventory.
+    await captureRunnerError(
+      planModuleMigrations({
+        aggregate: aggregate({ id: "core", migrations: [coreInitial] }),
+        database: new FakeMigrationDatabase({
+          history: [historyRecord(coreInitial, 1), historyRecord(coreGhost, 2)],
+        }),
+      }),
+      "MIGRATION_UNKNOWN_APPLIED",
+    );
+  });
+
+  it.each([
+    [
+      "an identity that does not name its own module and tag",
+      (source: DiscoveredModuleMigration) => [
+        historyRecord(source, 1, { identity: "calendar:0099_elsewhere" }),
+      ],
+    ],
+    [
+      "a duplicate applied order",
+      (source: DiscoveredModuleMigration) => [
+        historyRecord(source, 1),
+        historyRecord(migration("calendar", 1), 1),
+      ],
+    ],
+    [
+      "a duplicate index",
+      (source: DiscoveredModuleMigration) => [
+        historyRecord(source, 1),
+        historyRecord(migration("calendar", 1), 2, { index: 0 }),
+      ],
+    ],
+  ])("still rejects retained rows with %s", async (_label, makeHistory) => {
+    const database = new FakeMigrationDatabase({
+      history: makeHistory(migration("calendar", 0)),
+    });
+
+    await captureRunnerError(
+      planModuleMigrations({ aggregate: aggregate(), database }),
+      "MIGRATION_HISTORY_INVALID",
+    );
+  });
+
+  it("rejects a retained row that claims a present module's migration identity", async () => {
+    const peopleInitial = migration("people", 0);
+    const database = new FakeMigrationDatabase({
+      history: [historyRecord(peopleInitial, 1, { moduleId: "calendar" })],
+    });
+
+    await captureRunnerError(
+      planModuleMigrations({
+        aggregate: aggregate({ id: "people", migrations: [peopleInitial] }),
+        database,
+      }),
+      "MIGRATION_HISTORY_INVALID",
+    );
+  });
+});

core/tests/modules-directory-commands.test.ts

@@ -0,0 +1,116 @@
+import { cp, mkdtemp, readdir, readFile, rm } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import { afterEach, describe, expect, it } from "vitest";
+import { discoverRepositoryMigrations } from "../src/cli/migration-command-support.js";
+import { resolveCommandModulesDirectory } from "../src/cli/modules-directory-environment.js";
+import { ModuleDiscoveryError } from "../src/modules/index.js";
+
+const repositoryRoot = path.resolve(path.dirname(fileURLToPath(import.meta.url)), "..", "..");
+const templateModule = path.join(repositoryRoot, "templates", "module");
+const temporaryDirectories: string[] = [];
+
+afterEach(async () => {
+  await Promise.all(
+    temporaryDirectories.splice(0).map((directory) => rm(directory, { recursive: true })),
+  );
+});
+
+async function externalModulesDirectory(): Promise<string> {
+  const directory = await mkdtemp(path.join(tmpdir(), "ekklesia-installed-modules-"));
+  temporaryDirectories.push(directory);
+  return directory;
+}
+
+/** Installs the module template's migration-bearing package files as module `example`. Migration
+ * discovery imports nothing, so the template's manifest, package metadata, and migrations are all
+ * it reads; the compiled artifacts discovery checks for are copied too when they exist. */
+async function installTemplate(modulesDirectory: string): Promise<void> {
+  const target = path.join(modulesDirectory, "example");
+  for (const entry of ["package.json", "ekklesia.module.json", "drizzle", "dist"]) {
+    await cp(path.join(templateModule, entry), path.join(target, entry), { recursive: true });
+  }
+}
+
+describe("operator commands select the modules directory through host configuration", () => {
+  it("defaults to the repository's own modules directory", () => {
+    expect(resolveCommandModulesDirectory({}, "/opt/ekklesia")).toEqual({
+      modulesDirectory: "/opt/ekklesia/modules",
+      modulesDirectoryRequired: false,
+    });
+  });
+
+  it("honours EKKLESIA_MODULES_DIR", () => {
+    expect(
+      resolveCommandModulesDirectory(
+        { EKKLESIA_MODULES_DIR: "/var/lib/ekklesia/modules" },
+        "/opt/ekklesia",
+      ),
+    ).toEqual({ modulesDirectory: "/var/lib/ekklesia/modules", modulesDirectoryRequired: true });
+  });
+
+  it("refuses a relative EKKLESIA_MODULES_DIR without echoing it", () => {
+    expect(() =>
+      resolveCommandModulesDirectory({ EKKLESIA_MODULES_DIR: "modules-9e1f" }, "/opt/ekklesia"),
+    ).toThrow(ModuleDiscoveryError);
+    try {
+      resolveCommandModulesDirectory({ EKKLESIA_MODULES_DIR: "modules-9e1f" }, "/opt/ekklesia");
+    } catch (error) {
+      expect(JSON.stringify((error as ModuleDiscoveryError).issues)).not.toContain("9e1f");
+    }
+  });
+
+  it("plans migrations for modules installed outside the repository, with Core's from the platform", async () => {
+    const modulesDirectory = await externalModulesDirectory();
+    await installTemplate(modulesDirectory);
+
+    const aggregate = await discoverRepositoryMigrations(repositoryRoot, {
+      EKKLESIA_MODULES_DIR: modulesDirectory,
+    });
+
+    const sources = aggregate.modules.map((module) => module.moduleId);
+    expect(sources[0]).toBe("core");
+    expect(sources).toContain("example");
+    expect(
+      aggregate.migrations.some((migration) => migration.identity === "example:0000_initial"),
+    ).toBe(true);
+    const coreTags = (await readdir(path.join(repositoryRoot, "core", "drizzle"))).filter((name) =>
+      name.endsWith(".sql"),
+    );
+    expect(aggregate.modules[0]?.migrations).toHaveLength(coreTags.length);
+  });
+
+  it("fails closed when the configured directory does not exist", async () => {
+    const parent = await externalModulesDirectory();
+    await expect(
+      discoverRepositoryMigrations(repositoryRoot, {
+        EKKLESIA_MODULES_DIR: path.join(parent, "absent"),
+      }),
+    ).rejects.toBeInstanceOf(ModuleDiscoveryError);
+  });
+});
+
+describe("no source chooses a modules directory except the resolver", () => {
+  async function sourceFiles(directory: string): Promise<readonly string[]> {
+    const entries = await readdir(directory, { recursive: true, withFileTypes: true });
+    return entries
+      .filter((entry) => entry.isFile() && entry.name.endsWith(".ts"))
+      .map((entry) => path.join(entry.parentPath, entry.name));
+  }
+
+  it("never joins `modules` onto a root anywhere else in Core or the API", async () => {
+    const files = [
+      ...(await sourceFiles(path.join(repositoryRoot, "core", "src"))),
+      ...(await sourceFiles(path.join(repositoryRoot, "apps", "api", "src"))),
+    ];
+    const resolver = path.join(repositoryRoot, "core", "src", "modules", "modules-directory.ts");
+    for (const file of files) {
+      if (file === resolver) {
+        continue;
+      }
+      const text = await readFile(file, "utf8");
+      expect(text, path.relative(repositoryRoot, file)).not.toMatch(/,\s*"modules"\s*\)/u);
+    }
+  });
+});

core/tests/modules-directory.test.ts

@@ -0,0 +1,159 @@
+import { mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import {
+  discoverModules,
+  ModuleDiscoveryError,
+  type ModuleDiscoveryIssueCode,
+  resolveModulesDirectory,
+} from "../src/modules/index.js";
+
+const versions = { moduleSdkVersion: "0.1.0", platformVersion: "0.1.0" } as const;
+const repositoryRoot = path.join(path.sep, "opt", "ekklesia");
+const temporaryDirectories: string[] = [];
+
+afterEach(async () => {
+  await Promise.all(
+    temporaryDirectories.splice(0).map((directory) => rm(directory, { recursive: true })),
+  );
+});
+
+async function temporaryDirectory(): Promise<string> {
+  const directory = await mkdtemp(path.join(tmpdir(), "ekklesia-modules-directory-"));
+  temporaryDirectories.push(directory);
+  return directory;
+}
+
+function captureDiscoveryError(operation: () => unknown): ModuleDiscoveryError {
+  try {
+    operation();
+  } catch (error) {
+    expect(error).toBeInstanceOf(ModuleDiscoveryError);
+    return error as ModuleDiscoveryError;
+  }
+  throw new Error("Expected a ModuleDiscoveryError.");
+}
+
+async function captureAsyncDiscoveryError(
+  operation: Promise<unknown>,
+): Promise<ModuleDiscoveryError> {
+  try {
+    await operation;
+  } catch (error) {
+    expect(error).toBeInstanceOf(ModuleDiscoveryError);
+    return error as ModuleDiscoveryError;
+  }
+  throw new Error("Expected a ModuleDiscoveryError.");
+}
+
+function codes(error: ModuleDiscoveryError): readonly ModuleDiscoveryIssueCode[] {
+  return error.issues.map((issue) => issue.code);
+}
+
+/** Everything an operator, a log, or a test report could ever see from this error. */
+function rendered(error: ModuleDiscoveryError): string {
+  return JSON.stringify({ issues: error.issues, message: error.message, stack: error.stack });
+}
+
+describe("resolveModulesDirectory", () => {
+  it("defaults to the repository's own modules directory when nothing is configured", () => {
+    expect(resolveModulesDirectory({ configured: undefined, repositoryRoot })).toEqual({
+      modulesDirectory: path.join(repositoryRoot, "modules"),
+      modulesDirectoryRequired: false,
+    });
+  });
+
+  it("accepts an explicit absolute path, normalized, and requires it to exist", () => {
+    expect(
+      resolveModulesDirectory({ configured: "/var/lib/ekklesia/modules/", repositoryRoot }),
+    ).toEqual({ modulesDirectory: "/var/lib/ekklesia/modules", modulesDirectoryRequired: true });
+    expect(
+      resolveModulesDirectory({ configured: "/var/lib/./ekklesia//modules", repositoryRoot }),
+    ).toEqual({ modulesDirectory: "/var/lib/ekklesia/modules", modulesDirectoryRequired: true });
+  });
+
+  it("never resolves a configured path against the repository or the working directory", () => {
+    const resolved = resolveModulesDirectory({ configured: "/srv/modules", repositoryRoot });
+    expect(resolved.modulesDirectory).toBe("/srv/modules");
+  });
+
+  it.each([
+    ["a relative name", "modules"],
+    ["a dot-relative path", "./modules"],
+    ["a parent-relative path", "../private/modules"],
+    ["a home-relative path", "~/modules"],
+    ["the empty string", ""],
+    ["whitespace only", "   "],
+    ["an absolute path with surrounding whitespace", " /var/lib/ekklesia/modules"],
+    ["a NUL byte", "/var/lib/ekklesia/\u0000modules"],
+  ])("rejects %s with a sanitized MODULES_DIRECTORY_INVALID", (_label, configured) => {
+    const error = captureDiscoveryError(() =>
+      resolveModulesDirectory({ configured, repositoryRoot }),
+    );
+    expect(codes(error)).toEqual(["MODULES_DIRECTORY_INVALID"]);
+    expect(error.issues[0]?.message).toBe("EKKLESIA_MODULES_DIR must be an absolute path.");
+  });
+
+  it("never echoes the supplied value in the error", () => {
+    const configured = "relative/secret-token-a1b2c3/postgresql://admin:hunter2@db/modules";
+    const error = captureDiscoveryError(() =>
+      resolveModulesDirectory({ configured, repositoryRoot }),
+    );
+    const text = rendered(error);
+    expect(text).not.toContain("secret-token-a1b2c3");
+    expect(text).not.toContain("hunter2");
+    expect(text).not.toContain("relative/");
+  });
+});
+
+describe("module discovery against a configured modules directory", () => {
+  it("fails closed, without the path, when a configured directory does not exist", async () => {
+    const parent = await temporaryDirectory();
+    const missing = path.join(parent, "private-mount-name-7f3e");
+    const error = await captureAsyncDiscoveryError(
+      discoverModules({ ...versions, modulesDirectory: missing, modulesDirectoryRequired: true }),
+    );
+    expect(codes(error)).toEqual(["MODULES_DIRECTORY_UNREADABLE"]);
+    expect(rendered(error)).not.toContain("private-mount-name-7f3e");
+    expect(rendered(error)).not.toContain(parent);
+  });
+
+  it("fails closed when a configured path is a file rather than a directory", async () => {
+    const parent = await temporaryDirectory();
+    const file = path.join(parent, "modules");
+    await writeFile(file, "not a directory");
+    const error = await captureAsyncDiscoveryError(
+      discoverModules({ ...versions, modulesDirectory: file, modulesDirectoryRequired: true }),
+    );
+    expect(codes(error)).toEqual(["MODULES_DIRECTORY_UNREADABLE"]);
+    expect(rendered(error)).not.toContain(parent);
+  });
+
+  it("rejects a relative configured path even when it bypasses the resolver", async () => {
+    const error = await captureAsyncDiscoveryError(
+      discoverModules({ ...versions, modulesDirectory: "modules", modulesDirectoryRequired: true }),
+    );
+    expect(codes(error)).toEqual(["MODULES_DIRECTORY_INVALID"]);
+  });
+
+  it("treats an existing, empty configured directory as zero installed modules", async () => {
+    const directory = await temporaryDirectory();
+    await expect(
+      discoverModules({ ...versions, modulesDirectory: directory, modulesDirectoryRequired: true }),
+    ).resolves.toEqual([]);
+  });
+
+  it("keeps the development default lenient: a missing default directory is zero modules", async () => {
+    const parent = await temporaryDirectory();
+    await expect(
+      discoverModules({ ...versions, modulesDirectory: path.join(parent, "modules") }),
+    ).resolves.toEqual([]);
+  });
+
+  it("discovers through the resolver's own selection unchanged", async () => {
+    const directory = await temporaryDirectory();
+    const selection = resolveModulesDirectory({ configured: directory, repositoryRoot });
+    await expect(discoverModules({ ...versions, ...selection })).resolves.toEqual([]);
+  });
+});

core/tests/postgres-migration.integration.ts

@@ -1,5 +1,7 @@
 import { createHash, randomBytes } from "node:crypto";
+import { cp, mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import net from "node:net";
+import { tmpdir } from "node:os";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
 import { Client, type QueryResult, type QueryResultRow } from "pg";
@@ -8,6 +10,7 @@ import { reportMigrationCommandError } from "../src/cli/migration-command-errors
 import {
   applyModuleMigrations,
   createPostgresMigrationDatabase,
+  discoverAllMigrations,
   discoverCoreMigrations,
   type MigrationApproval,
   type MigrationApprovalProvider,
@@ -764,7 +767,7 @@ describe.sequential("live PostgreSQL module migration execution", () => {
         database: migrationDatabase,
       });
 
-      expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true });
+      expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true, retained: [] });
       expect(await databaseState(database.client)).toEqual(before);
       const afterData = await safeQuery<QueryResultRow>(
         database.client,
@@ -834,7 +837,48 @@ describe.sequential("live PostgreSQL module migration execution", () => {
     });
   });
 
-  it("rejects an unknown applied identity without repair or further execution", async () => {
+  it("retains an absent module's history and still applies later work (ADR 0048)", async () => {
+    await withIsolatedDatabase("absent_history", async (database) => {
+      const initial = peopleInitial();
+      const later = peopleLater();
+      const initialInventory = aggregate(moduleFixture("people", [initial]));
+      const completeInventory = aggregate(moduleFixture("people", [initial, later]));
+      const migrationDatabase = createPostgresMigrationDatabase(database.url);
+      await applyModuleMigrations({ aggregate: initialInventory, database: migrationDatabase });
+      // History left by a module that is no longer installed: kept, reported, never fatal.
+      await safeQuery(
+        database.client,
+        `
+          INSERT INTO public.ekklesia_core_migrations
+            (identity, module_id, migration_tag, migration_index, checksum)
+          VALUES ($1, $2, $3, $4, $5)
+        `,
+        ["ghost:0000_unknown", "ghost", "0000_unknown", 0, "f".repeat(64)],
+      );
+
+      const plan = await planModuleMigrations({
+        aggregate: completeInventory,
+        database: migrationDatabase,
+      });
+      expect(plan.retained).toEqual([{ appliedCount: 1, moduleId: "ghost" }]);
+      expect(plan.pendingCount).toBe(1);
+
+      const result = await applyModuleMigrations({
+        aggregate: completeInventory,
+        database: migrationDatabase,
+      });
+      expect(result.applied.map((migration) => migration.identity)).toEqual([later.identity]);
+      expect(result.retained).toEqual([{ appliedCount: 1, moduleId: "ghost" }]);
+      expect(await columnExists(database.client, "people_records", "email")).toBe(true);
+      expect((await readHistory(database.client)).map((row) => row.identity)).toEqual([
+        initial.identity,
+        "ghost:0000_unknown",
+        later.identity,
+      ]);
+    });
+  });
+
+  it("rejects an unknown applied identity of an installed module without repair or further execution", async () => {
     await withIsolatedDatabase("unknown_history", async (database) => {
       const initial = peopleInitial();
       const later = peopleLater();
@@ -849,7 +893,7 @@ describe.sequential("live PostgreSQL module migration execution", () => {
             (identity, module_id, migration_tag, migration_index, checksum)
           VALUES ($1, $2, $3, $4, $5)
         `,
-        ["ghost:0000_unknown", "ghost", "0000_unknown", 0, "f".repeat(64)],
+        ["people:0099_unknown", "people", "0099_unknown", 99, "f".repeat(64)],
       );
       const corrupted = await databaseState(database.client);
 
@@ -866,7 +910,7 @@ describe.sequential("live PostgreSQL module migration execution", () => {
       expect(await columnExists(database.client, "people_records", "email")).toBe(false);
       expect((await readHistory(database.client)).map((row) => row.identity)).toEqual([
         initial.identity,
-        "ghost:0000_unknown",
+        "people:0099_unknown",
       ]);
     });
   });
@@ -1358,7 +1402,7 @@ describe.sequential("live PostgreSQL Core identity migration execution", () => {
         database: migrationDatabase,
       });
 
-      expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true });
+      expect(result).toEqual({ applied: [], appliedCount: 0, noOp: true, retained: [] });
       expect(await databaseState(database.client)).toEqual(before);
     });
   });
@@ -1851,3 +1895,151 @@ describe.sequential("live PostgreSQL migration timeout precedence", () => {
     });
   });
 });
+
+/**
+ * ADR 0048 end to end, with real discovery: Core's committed migrations, the module template
+ * installed in a modules directory outside the repository, and a real PostgreSQL. Core's newest
+ * migration is withheld from a copy of `core/drizzle` at first, so a genuinely later Core migration
+ * can be applied while the module is absent.
+ */
+describe.sequential("live PostgreSQL retained history for an uninstalled module", () => {
+  const repositoryRoot = path.resolve(path.dirname(fileURLToPath(import.meta.url)), "..", "..");
+  const templateModule = path.join(repositoryRoot, "templates", "module");
+  const versions = { moduleSdkVersion: "0.1.0", platformVersion: "0.1.0" } as const;
+
+  async function coreWithoutNewestMigration(directory: string): Promise<string> {
+    const target = path.join(directory, "core-drizzle");
+    await cp(coreMigrationsDirectory, target, { recursive: true });
+    const journalPath = path.join(target, "meta", "_journal.json");
+    const policyPath = path.join(target, "meta", "_ekklesia.json");
+    const journal = JSON.parse(await readFile(journalPath, "utf8")) as {
+      entries: { idx: number; tag: string }[];
+    };
+    const policy = JSON.parse(await readFile(policyPath, "utf8")) as { entries: unknown[] };
+    const newest = journal.entries.pop();
+    policy.entries.pop();
+    if (!newest) {
+      throw harnessError("Core has no migration to withhold.");
+    }
+    await writeFile(journalPath, `${JSON.stringify(journal, null, 2)}\n`);
+    await writeFile(policyPath, `${JSON.stringify(policy, null, 2)}\n`);
+    await rm(path.join(target, `${newest.tag}.sql`));
+    await rm(path.join(target, "meta", `${String(newest.idx).padStart(4, "0")}_snapshot.json`));
+    return target;
+  }
+
+  async function installExample(modulesDirectory: string): Promise<void> {
+    for (const entry of ["package.json", "ekklesia.module.json", "drizzle", "dist"]) {
+      await cp(path.join(templateModule, entry), path.join(modulesDirectory, "example", entry), {
+        recursive: true,
+      });
+    }
+  }
+
+  async function inventory(coreDirectory: string, modulesDirectory: string) {
+    return discoverAllMigrations({
+      coreMigrationsDirectory: coreDirectory,
+      moduleDiscovery: { ...versions, modulesDirectory, modulesDirectoryRequired: true },
+    });
+  }
+
+  async function exampleValues(client: Client): Promise<readonly string[]> {
+    const result = await safeQuery<{ readonly value: string } & QueryResultRow>(
+      client,
+      "SELECT value FROM public.example_records ORDER BY value",
+    );
+    return result.rows.map((row) => row.value);
+  }
+
+  it("keeps an uninstalled module's data and history, applies later Core work, and restores it", async () => {
+    const scratch = await mkdtemp(path.join(tmpdir(), "ekklesia-retained-history-"));
+    try {
+      const earlyCore = await coreWithoutNewestMigration(scratch);
+      const modulesDirectory = path.join(scratch, "modules");
+      await mkdir(modulesDirectory);
+      await installExample(modulesDirectory);
+
+      await withIsolatedDatabase("retained_module", async (database) => {
+        const migrationDatabase = createPostgresMigrationDatabase(database.url);
+
+        // 1. Core (minus its newest migration) and the installed module, applied together.
+        const first = await applyModuleMigrations({
+          aggregate: await inventory(earlyCore, modulesDirectory),
+          database: migrationDatabase,
+        });
+        expect(first.applied.map((migration) => migration.identity)).toContain(
+          "example:0000_initial",
+        );
+        expect(first.retained).toEqual([]);
+
+        // 2. Module-owned data.
+        await safeQuery(
+          database.client,
+          "INSERT INTO public.example_records (id, value) VALUES (gen_random_uuid(), 'kept')",
+        );
+
+        // 3. The module is uninstalled: its directory is gone from module storage.
+        await rm(path.join(modulesDirectory, "example"), { recursive: true });
+
+        // 4. A later Core migration plans and applies while the module is absent.
+        const absentInventory = await inventory(coreMigrationsDirectory, modulesDirectory);
+        const absentPlan = await planModuleMigrations({
+          aggregate: absentInventory,
+          database: migrationDatabase,
+        });
+        expect(absentPlan.retained).toEqual([{ appliedCount: 1, moduleId: "example" }]);
+        expect(
+          absentPlan.entries.filter((entry) => entry.status === "pending").map((e) => e.moduleId),
+        ).toEqual(["core"]);
+        const later = await applyModuleMigrations({
+          aggregate: absentInventory,
+          database: migrationDatabase,
+        });
+        expect(later.applied).toHaveLength(1);
+        expect(later.applied[0]?.moduleId).toBe("core");
+        expect(later.retained).toEqual([{ appliedCount: 1, moduleId: "example" }]);
+
+        // 5. The module's table and rows are untouched, and so is its history.
+        expect(await exampleValues(database.client)).toEqual(["kept"]);
+        expect((await readHistory(database.client)).map((row) => row.identity)).toContain(
+          "example:0000_initial",
+        );
+
+        // 6. The module is reinstalled.
+        await installExample(modulesDirectory);
+        const restored = await inventory(coreMigrationsDirectory, modulesDirectory);
+
+        // 7. Its history is strict again, and valid; its data is where it left it.
+        const restoredPlan = await planModuleMigrations({
+          aggregate: restored,
+          database: migrationDatabase,
+        });
+        expect(restoredPlan.retained).toEqual([]);
+        expect(restoredPlan.pendingCount).toBe(0);
+        expect(
+          restoredPlan.entries.find((entry) => entry.identity === "example:0000_initial")?.status,
+        ).toBe("applied");
+        const noOp = await applyModuleMigrations({
+          aggregate: restored,
+          database: migrationDatabase,
+        });
+        expect(noOp.noOp).toBe(true);
+        expect(await exampleValues(database.client)).toEqual(["kept"]);
+
+        // A returning package whose applied migration changed is refused, exactly as before.
+        const sqlPath = path.join(modulesDirectory, "example", "drizzle", "0000_initial.sql");
+        await writeFile(sqlPath, `${await readFile(sqlPath, "utf8")}-- edited\n`);
+        await captureRunnerError(
+          planModuleMigrations({
+            aggregate: await inventory(coreMigrationsDirectory, modulesDirectory),
+            database: migrationDatabase,
+          }),
+          "MIGRATION_CHECKSUM_MISMATCH",
+        );
+        expect(await exampleValues(database.client)).toEqual(["kept"]);
+      });
+    } finally {
+      await rm(scratch, { recursive: true, force: true });
+    }
+  });
+});