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/api-server/routes-work-graph.ts

@@ -256,7 +256,7 @@ export function registerWorkGraphRoutes(server: AgentApiServer) {
       server.json(res, 403, { error: "Company mismatch" });
       return;
     }
-    const { agents, tasks, recentActivity } = db.getDashboardSnapshot(companyId);
+    const { agents, tasks, recentActivity } = db.company.getDashboardSnapshot(companyId);
 
     const tasksByStatus: Record<string, number> = {};
     for (const t of tasks) {