feat: todo lists, permission modes, project instructions, and agent robustness

- Add todo_write tool with live checklist rendering in the UI
- Add permission modes (default/plan/auto-edit/auto-accept) cycled via Shift+Tab or /perm
- Load CLAUDE.md/AGENTS.md as project instructions into the system prompt
- Forward sub-agent tool calls/results to parent UI panel
- Auto-compact context mid-turn and keep model moving with a synthetic user turn
- Prune older image_url parts to cap vision token cost
- Idle-abort guard for stalled streaming backends
- Improve background bash jobs, kill whole process trees on timeout/exit
- Expand hooks: command/http hooks, blocking, JSON outputSchema
- MCP: JSON schema → Zod conversion, parallel connection, duplicate server detection
- Add tests for loop, confirmFn, projectInstructions, readFile, bash, todoWrite, contextWindowCache

src/cli.ts

@@ -114,7 +114,7 @@ configCmd
 
 configCmd
   .command("set <key> <value>")
-  .description("Persist a config value (backend, model, baseUrl, contextWindow, maxIterations, autoCompactThreshold, requestTimeoutMs)")
+  .description("Persist a config value (backend, model, baseUrl, contextWindow, maxIterations, autoCompactThreshold, requestTimeoutMs, subagentTimeoutMs)")
   .action((key: string, value: string) => {
     if (
       key !== "backend" &&
@@ -123,10 +123,11 @@ configCmd
       key !== "contextWindow" &&
       key !== "maxIterations" &&
       key !== "autoCompactThreshold" &&
-      key !== "requestTimeoutMs"
+      key !== "requestTimeoutMs" &&
+      key !== "subagentTimeoutMs"
     ) {
       console.error(
-        `Unknown config key "${key}". Valid keys: backend, model, baseUrl, contextWindow, maxIterations, autoCompactThreshold, requestTimeoutMs`,
+        `Unknown config key "${key}". Valid keys: backend, model, baseUrl, contextWindow, maxIterations, autoCompactThreshold, requestTimeoutMs, subagentTimeoutMs`,
       );
       process.exit(1);
     }
@@ -152,6 +153,13 @@ configCmd
         process.exit(1);
       }
       stored[key] = n;
+    } else if (key === "subagentTimeoutMs") {
+      const n = Number(value);
+      if (!Number.isFinite(n) || n < 1_000 || n > 3_600_000) {
+        console.error(`subagentTimeoutMs must be between 1000 and 3600000, got "${value}".`);
+        process.exit(1);
+      }
+      stored[key] = n;
     } else {
       stored[key] = value;
     }