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/cost-writer.ts

@@ -45,7 +45,7 @@ export class CostWriter {
       );
     }
 
-    this.deps.db.recordCostEntry({
+    this.deps.db.runs.recordCostEntry({
       runId: input.runId,
       companyId: input.companyId,
       agentId: input.agentId,

src/main/agent-runtime/hook-handlers.ts

@@ -134,7 +134,7 @@ function checkOperationalApprovalBlock(
   toolName: string,
 ): BeforeToolCallRpcResult {
   try {
-    const blocking = deps.db.getBlockingApproval(ctx.companyId, ctx.agentId, ctx.taskId);
+    const blocking = deps.db.approvalsMod.getBlockingApproval(ctx.companyId, ctx.agentId, ctx.taskId);
     if (!blocking) return { block: false, reason: null };
     if (!OPERATIONAL_APPROVAL_TYPES.has(blocking.type as ApprovalType)) {
       return { block: false, reason: null };

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) {