feat(v2): add permission mode passthrough and fix agent stop-on-close

- Add permission_mode field to AgentQueryOptions (Rust, sidecar, bridge)
  flowing from controller through sidecar to SDK; defaults to
  bypassPermissions, supports default mode
- Fix AgentPane onDestroy bug: remove stopAgent() from onDestroy (fires
  on layout remounts), move stop-on-close to TilingGrid onClose handler
- Bundle SDK into sidecar via esbuild (remove --external flag)

v2/sidecar/agent-runner-deno.ts

@@ -27,6 +27,7 @@ interface QueryMessage {
   maxTurns?: number;
   maxBudgetUsd?: number;
   resumeSessionId?: string;
+  permissionMode?: string;
 }
 
 interface StopMessage {
@@ -51,7 +52,7 @@ function handleMessage(msg: Record<string, unknown>) {
 }
 
 async function handleQuery(msg: QueryMessage) {
-  const { sessionId, prompt, cwd, maxTurns, maxBudgetUsd, resumeSessionId } = msg;
+  const { sessionId, prompt, cwd, maxTurns, maxBudgetUsd, resumeSessionId, permissionMode } = msg;
 
   if (sessions.has(sessionId)) {
     send({ type: "error", sessionId, message: "Session already running" });
@@ -84,8 +85,8 @@ async function handleQuery(msg: QueryMessage) {
           "Bash", "Read", "Write", "Edit", "Glob", "Grep",
           "WebSearch", "WebFetch", "TodoWrite", "NotebookEdit",
         ],
-        permissionMode: "bypassPermissions",
-        allowDangerouslySkipPermissions: true,
+        permissionMode: (permissionMode ?? "bypassPermissions") as "bypassPermissions" | "default",
+        allowDangerouslySkipPermissions: (permissionMode ?? "bypassPermissions") === "bypassPermissions",
       },
     });