Codemod db pass-through calls to domain modules: tasks + agents (C1 part 1/3)

Rewrite ~525 call sites from `db.<method>()` to `db.<module>.<method>()`
for tasks and agents domains (including `getAgent`/`findAgent`/`getTask`
which live on the `entityCrud` field). Delete the corresponding
pass-through methods on AppDatabaseBase. Structural types that narrowed
`db` to a bag of flat methods (CapabilityMatchDb, EscalationDeps,
SweepStaleReviewsDeps) are reshaped to match the new namespace. Internal
callback references inside database.ts/database-base.ts now invoke the
owning module directly (e.g. `this.agents.saveAgent`) rather than the
deleted pass-through.

The codemod lives at scripts/codemod/remove-appdatabase-passthrough.mjs
and filters by owning module + optional explicit method list. It is
idempotent and does not re-rewrite already-namespaced calls.

tests/integration/autonomous-chain/shared-setup.ts

@@ -30,7 +30,7 @@ export interface SharedHandle {
   set db(value: AppDatabase);
   get companyId(): string;
   get workspaceId(): string;
-  createAgent(overrides?: Partial<Parameters<AppDatabase["saveAgent"]>[0]>): string;
+  createAgent(overrides?: Partial<Parameters<AppDatabase["agents"]["saveAgent"]>[0]>): string;
   buildCtx(overrides?: Record<string, unknown>): Parameters<typeof buildSystemPrompt>[0];
   tempDirs: string[];
 }
@@ -80,8 +80,8 @@ export function installSharedSetup(): SharedHandle {
     return state.db;
   }
 
-  function createAgent(overrides: Partial<Parameters<AppDatabase["saveAgent"]>[0]> = {}): string {
-    return currentDb().saveAgent({
+  function createAgent(overrides: Partial<Parameters<AppDatabase["agents"]["saveAgent"]>[0]> = {}): string {
+    return currentDb().agents.saveAgent({
       companyId: state.companyId,
       name: "TestAgent",
       role: "CEO",
@@ -98,7 +98,7 @@ export function installSharedSetup(): SharedHandle {
   }
 
   function buildCtx(overrides: Record<string, unknown> = {}): Parameters<typeof buildSystemPrompt>[0] {
-    const agent = currentDb().getAgent(overrides.agentId as string ?? createAgent());
+    const agent = currentDb().entityCrud.getAgent(overrides.agentId as string ?? createAgent());
     return {
       agent,
       apiUrl: "http://127.0.0.1:3000",