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/skill-aware-assignment.spec.ts

@@ -32,7 +32,7 @@ describe("skill-aware capability registry", () => {
       lastError: null,
     });
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Skill Match Co",
       description: "Tests skill-aware assignment",
       status: "active",
@@ -122,7 +122,7 @@ describe("skill-aware capability registry", () => {
       lastError: null,
     });
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Registry Co",
       description: "Tests capability registry prompt injection",
       status: "active",