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/messaging/dispatch.ts

@@ -184,7 +184,7 @@ export function validateAgentMessageInput(
   }
 
   if (input.parentMessageId) {
-    const parentMessage = db.getAgentMessage(input.parentMessageId, input.companyId);
+    const parentMessage = db.messages.getAgentMessage(input.parentMessageId, input.companyId);
     if (!parentMessage) {
       return {
         code: "PARENT_MESSAGE_NOT_FOUND",
@@ -317,8 +317,8 @@ export function dispatchAgentMessage(
   const persistedMessage = normalized.channel === "direct"
     ? { ...normalized, senderKind, mentionedAgentIds }
     : { ...normalized, toAgentId: null, senderKind, mentionedAgentIds };
-  const id = deps.db.sendAgentMessage(persistedMessage);
-  const message = deps.db.getAgentMessage(id, normalized.companyId);
+  const id = deps.db.messages.sendAgentMessage(persistedMessage);
+  const message = deps.db.messages.getAgentMessage(id, normalized.companyId);
   if (message && deps.emitEvent) {
     deps.emitEvent({ type: "new-message", message });
   }