Codemod db pass-through calls: messages + runs + approvals + company (C1 part 2/3)

Rewrite ~376 call sites for messages, runs, approvalsMod, and company
domains and delete the corresponding pass-through methods on
AppDatabase / AppDatabaseBase. Structural type references
(ReturnType<HandlerDeps["db"]["getRun"]>) and SweepStaleReviewsDeps-style
mocks are updated to route through the owning sub-module.

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

@@ -54,7 +54,7 @@ export function installSharedSetup(): SharedHandle {
     state.db = new AppDatabase(profileDir);
     state.db.init();
 
-    state.companyId = state.db.saveCompany({
+    state.companyId = state.db.company.saveCompany({
       name: "Autonomous Test Corp",
       description: "Test company for autonomous chain",
       status: "active",