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.

src/main/agent-runtime/runtime-bridge.ts

@@ -573,7 +573,7 @@ export class RuntimeBridge {
     // `?unreadOnly=true`, so agents posted status comments instead of
     // replies. The explicit read endpoint is the sole signal.
     const store = this.getOrCreateStore(payload.taskSessionId);
-    const inboxRecords = this.deps.db.listAgentInboxUnread(payload.companyId, payload.agentId);
+    const inboxRecords = this.deps.db.messages.listAgentInboxUnread(payload.companyId, payload.agentId);
     if (inboxRecords.length > 0) {
       this.deps.db.withTransaction(() => {
         for (const record of inboxRecords) {