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/src/migrations/runner.ts

@@ -2,6 +2,7 @@ import type {
   DiscoveredModuleMigration,
   ModuleMigrationAggregate,
 } from "../modules/migration-discovery.js";
+import { CORE_MIGRATION_SOURCE_ID } from "./core-source.js";
 
 const DEFAULT_MIGRATION_LOCK_TIMEOUT_MS = 10_000;
 
@@ -86,11 +87,24 @@ export interface MigrationPlanEntry {
   readonly tag: string;
 }
 
+/**
+ * Applied history kept for a module that is not installed (ADR 0048): the module id and how many of
+ * its migrations were applied. It is reported, never matched against an inventory, and never a
+ * reason to refuse planning or applying anything else.
+ */
+export interface RetainedMigrationHistory {
+  readonly appliedCount: number;
+  readonly moduleId: string;
+}
+
 export interface MigrationPlanResult {
   readonly appliedCount: number;
   readonly approvalRequiredCount: number;
   readonly entries: readonly MigrationPlanEntry[];
   readonly pendingCount: number;
+  /** Absent modules' applied history, ordered by module id; empty when every applied migration
+   * belongs to Core or an installed module. */
+  readonly retained: readonly RetainedMigrationHistory[];
 }
 
 export interface AppliedMigrationResult {
@@ -105,6 +119,8 @@ export interface MigrationApplyResult {
   readonly applied: readonly AppliedMigrationResult[];
   readonly appliedCount: number;
   readonly noOp: boolean;
+  /** The same report as `MigrationPlanResult.retained`, read under the migration lock. */
+  readonly retained: readonly RetainedMigrationHistory[];
 }
 
 export interface PlanModuleMigrationsOptions {
@@ -204,10 +220,38 @@ function validateHistoryRecordShape(record: AppliedMigrationRecord): void {
   }
 }
 
+interface ValidatedAppliedHistory {
+  /** Identities of applied migrations that belong to Core or an installed module. */
+  readonly applied: ReadonlySet<string>;
+  readonly retained: readonly RetainedMigrationHistory[];
+}
+
+/**
+ * Every module id this inventory treats as installed: each discovered module, whether or not it
+ * owns migrations, every module that contributed migrations, and always Core. A module counts as
+ * absent only when it is none of these, so a module that is installed but no longer ships its old
+ * migrations stays strict, and Core's history can never be classified as an absent module's.
+ */
+function installedMigrationSources(aggregate: ModuleMigrationAggregate): ReadonlySet<string> {
+  return new Set<string>([
+    CORE_MIGRATION_SOURCE_ID,
+    ...aggregate.discoveredModules.map((module) => module.manifest.id),
+    ...aggregate.modules.map((module) => module.moduleId),
+  ]);
+}
+
+function freezeRetained(counts: ReadonlyMap<string, number>): readonly RetainedMigrationHistory[] {
+  return Object.freeze(
+    [...counts.entries()]
+      .sort(([left], [right]) => (left < right ? -1 : left > right ? 1 : 0))
+      .map(([moduleId, appliedCount]) => Object.freeze({ appliedCount, moduleId })),
+  );
+}
+
 function validateAppliedHistoryUnchecked(
   aggregate: ModuleMigrationAggregate,
   history: readonly AppliedMigrationRecord[],
-): ReadonlySet<string> {
+): ValidatedAppliedHistory {
   if (!Array.isArray(history)) {
     throw runnerError("MIGRATION_HISTORY_INVALID");
   }
@@ -215,6 +259,9 @@ function validateAppliedHistoryUnchecked(
   const inventory = new Map(
     aggregate.migrations.map((migration) => [migration.identity, migration]),
   );
+  const installed = installedMigrationSources(aggregate);
+  const applied = new Set<string>();
+  const retained = new Map<string, number>();
   const seenOrders = new Set<number>();
   const seenIdentities = new Set<string>();
   const seenModuleIndexes = new Set<string>();
@@ -240,7 +287,19 @@ function validateAppliedHistoryUnchecked(
 
     const migration = knownMigration(inventory, record.identity);
     if (!migration) {
-      throw runnerError("MIGRATION_UNKNOWN_APPLIED");
+      if (installed.has(record.moduleId)) {
+        // Core, or a module that is installed now: its history is strict, exactly as ADR 0009
+        // established. A migration it no longer ships is a downgrade or a rewritten package.
+        throw runnerError("MIGRATION_UNKNOWN_APPLIED");
+      }
+      // An absent module's history (ADR 0048): retained and reported, never repaired, deleted, or
+      // matched against anything. It must still name its own module and tag, so a corrupt row is
+      // never mistaken for one.
+      if (record.identity !== `${record.moduleId}:${record.tag}`) {
+        throw runnerError("MIGRATION_HISTORY_INVALID");
+      }
+      retained.set(record.moduleId, (retained.get(record.moduleId) ?? 0) + 1);
+      continue;
     }
     if (
       record.moduleId !== migration.moduleId ||
@@ -252,11 +311,12 @@ function validateAppliedHistoryUnchecked(
     if (record.checksum !== migration.checksum) {
       throw runnerError("MIGRATION_CHECKSUM_MISMATCH", migration.identity);
     }
+    applied.add(record.identity);
   }
 
   for (const module of aggregate.modules) {
-    const applied = history.filter((record) => record.moduleId === module.moduleId);
-    for (const [position, record] of applied.entries()) {
+    const moduleHistory = history.filter((record) => record.moduleId === module.moduleId);
+    for (const [position, record] of moduleHistory.entries()) {
       if (record.identity !== module.migrations[position]?.identity) {
         const migration = knownMigration(inventory, record.identity);
         throw runnerError("MIGRATION_HISTORY_INVALID", migration?.identity);
@@ -264,13 +324,13 @@ function validateAppliedHistoryUnchecked(
     }
   }
 
-  return seenIdentities;
+  return Object.freeze({ applied, retained: freezeRetained(retained) });
 }
 
 function validateAppliedHistory(
   aggregate: ModuleMigrationAggregate,
   history: readonly AppliedMigrationRecord[],
-): ReadonlySet<string> {
+): ValidatedAppliedHistory {
   try {
     return validateAppliedHistoryUnchecked(aggregate, history);
   } catch (error) {
@@ -285,7 +345,7 @@ function planFromHistory(
   aggregate: ModuleMigrationAggregate,
   history: readonly AppliedMigrationRecord[],
 ): MigrationPlanResult {
-  const applied = validateAppliedHistory(aggregate, history);
+  const { applied, retained } = validateAppliedHistory(aggregate, history);
   const entries = Object.freeze(
     aggregate.migrations.map((migration): MigrationPlanEntry => {
       const isApplied = applied.has(migration.identity);
@@ -314,6 +374,7 @@ function planFromHistory(
     approvalRequiredCount,
     entries,
     pendingCount: entries.length - appliedCount,
+    retained,
   });
 }
 
@@ -472,14 +533,14 @@ export async function applyModuleMigrations(
     } catch {
       throw runnerError("MIGRATION_HISTORY_READ_FAILED");
     }
-    const applied = validateAppliedHistory(options.aggregate, history);
+    const { applied, retained } = validateAppliedHistory(options.aggregate, history);
     const pending = Object.freeze(
       options.aggregate.migrations.filter((migration) => !applied.has(migration.identity)),
     );
     await preflightApprovals(pending, options.approvals ?? denyAllMigrationApprovals);
 
     if (pending.length === 0) {
-      return Object.freeze({ applied: Object.freeze([]), appliedCount: 0, noOp: true });
+      return Object.freeze({ applied: Object.freeze([]), appliedCount: 0, noOp: true, retained });
     }
 
     let executingIdentity: string | undefined;
@@ -508,6 +569,7 @@ export async function applyModuleMigrations(
       applied: resultMigrations,
       appliedCount: resultMigrations.length,
       noOp: false,
+      retained,
     });
   } catch (error) {
     primaryError = error;