feat: Add "bypass permissions" mode + execution mode selector (#645)

### What changed?

Adding "bypassPermissions" execution mode to allow Claude to skip permission prompts. Can't live without it. Addresses #645.

![Screenshot 2026-01-27 at 13.55.14.png](https://app.graphite.com/user-attachments/assets/99693973-2dac-44c8-aa53-683c35e1ee67.png)

-----

I hijacked your PRs @Twixes, love this 100%! 🥇 

I disabled it by default and put it behind a setting, when they enable the setting I also give them a talking to about safe AI usage 😆

Similar flow to claude code w/ ``claude --dangerously-skip-permissions``, will be a once-on type thing for power users. We are starting to onboarding early adopters and Jonathan working on revamping the permissions persistence and prompt, so I wanna make sure we have good happy paths here.

Was able to fix merge conflicts, tests + lint, we should be able to get this in soon! Let me know any thoughts/feedback

<img width="595" height="164" alt="Screenshot 2026-01-27 at 2 00 57 PM" src="https://github.com/user-attachments/assets/8f7d2a7d-63ca-4807-8acd-d34e286d52b6" />
<img width="544" height="378" alt="Screenshot 2026-01-27 at 1 59 54 PM" src="https://github.com/user-attachments/assets/2612b96e-7cea-453c-b8fc-af31158faddc" />

Author: Twixes

PROBLEM.md

@@ -0,0 +1,82 @@
+# Agent Process Lifecycle Bug
+
+## Problem Summary
+
+Multiple interrelated bugs causing:
+1. **Duplicate agents** - Multiple agent processes run for same task, causing interleaved responses
+2. **App hangs on shutdown** - Cleanup waits indefinitely for unresponsive agent processes
+3. **Orphaned processes** - Agent subprocesses not properly terminated
+
+## Root Causes
+
+### Race Condition #1: Renderer (sessionStore.ts:955-1012)
+```typescript
+if (connectAttempts.has(taskId)) return;  // Line 956 - check
+// ... async work ...
+connectAttempts.add(taskId);               // Line 1012 - add (too late!)
+```
+Two rapid calls both pass the check before either adds to the set.
+
+### Race Condition #2: Main Process (service.ts:388-497)
+```typescript
+const existing = this.sessions.get(taskRunId);  // Line 389 - check
+if (existing) return existing;
+// ... 100+ lines of async work ...
+this.sessions.set(taskRunId, session);          // Line 497 - set (too late!)
+```
+Also: Sessions keyed by `taskRunId`, not `taskId` - two runs for same task both create agents.
+
+### No Cleanup Timeout (app-lifecycle/service.ts:22-40)
+```typescript
+await container.unbindAll();  // Line 26 - can hang forever
+```
+If agent subprocess doesn't respond, cleanup never completes, app never quits.
+
+---
+
+## Key Files
+
+| File | Role |
+|------|------|
+| `apps/twig/src/main/services/agent/service.ts` | Main process agent management - sessions Map, getOrCreateSession, cleanupSession |
+| `apps/twig/src/renderer/features/sessions/stores/sessionStore.ts` | Renderer session management - connectAttempts Set, connectToTask |
+| `apps/twig/src/main/services/app-lifecycle/service.ts` | App shutdown - calls container.unbindAll() |
+| `packages/agent/src/agent.ts` | Agent wrapper - cleanup() method |
+| `packages/agent/src/adapters/acp-connection.ts` | ACP connection - actual cleanup logic |
+
+---
+
+## Fix Plan
+
+### Phase 1: Main Process Mutex + Kill-Before-Create
+- Add `sessionsByTaskId` Map to track by taskId (not just taskRunId)
+- Add `pendingCreations` Map to prevent race conditions
+- Before creating new session, clean up any existing session for same taskId
+
+### Phase 2: Cleanup Timeout
+- Race `agent.cleanup()` against 5-second timeout
+- Call `forceCleanup()` if timeout
+
+### Phase 3: Force Cleanup Method
+- Add `forceCleanup()` to Agent class that aborts the session controller
+
+### Phase 4: App Shutdown Timeout
+- Add 10-second overall timeout to `shutdown()`
+
+### Phase 5: Renderer Mutex
+- Replace `connectAttempts` Set with Promise-based locking
+- Check "connecting" status, not just "connected"
+
+---
+
+## Debug Log Location
+
+When the app hangs on shutdown, check:
+```
+~/Library/Logs/twig/main.log
+```
+
+Or tail it live:
+```bash
+tail -f ~/Library/Logs/twig/main.log | grep -E "(AGENT_DEBUG|cleanupSession|getOrCreateSession|shutdown)"
+```

apps/twig/src/main/services/agent/schemas.ts

@@ -2,6 +2,7 @@ import type {
   RequestPermissionRequest,
   PermissionOption as SdkPermissionOption,
 } from "@agentclientprotocol/sdk";
+import { executionModeSchema } from "@shared/types";
 import { z } from "zod";
 
 // Session credentials schema
@@ -13,10 +14,6 @@ export const credentialsSchema = z.object({
 
 export type Credentials = z.infer<typeof credentialsSchema>;
 
-// Execution mode schema
-export const executionModeSchema = z.enum(["plan", "acceptEdits", "default"]);
-export type ExecutionMode = z.infer<typeof executionModeSchema>;
-
 // Session config schema
 export const sessionConfigSchema = z.object({
   taskId: z.string(),
@@ -45,7 +42,9 @@ export const startSessionInput = z.object({
   permissionMode: z.string().optional(),
   autoProgress: z.boolean().optional(),
   model: z.string().optional(),
-  executionMode: z.enum(["plan", "acceptEdits", "default"]).optional(),
+  executionMode: z
+    .enum(["default", "acceptEdits", "plan", "bypassPermissions"])
+    .optional(),
   runMode: z.enum(["local", "cloud"]).optional(),
   /** Additional directories Claude can access beyond cwd (for worktree support) */
   additionalDirectories: z.array(z.string()).optional(),
@@ -146,7 +145,7 @@ export const setModelInput = z.object({
 // Set mode input
 export const setModeInput = z.object({
   sessionId: z.string(),
-  modeId: z.enum(["plan", "default", "acceptEdits"]),
+  modeId: executionModeSchema,
 });
 
 // Subscribe to session events input

apps/twig/src/main/services/agent/service.ts

@@ -20,6 +20,7 @@ import { getLlmGatewayUrl } from "@posthog/agent/posthog-api";
 import type { OnLogCallback } from "@posthog/agent/types";
 import { app } from "electron";
 import { injectable, preDestroy } from "inversify";
+import type { ExecutionMode } from "@/shared/types.js";
 import type { AcpMessage } from "../../../shared/types/session-events.js";
 import { logger } from "../../lib/logger.js";
 import { TypedEventEmitter } from "../../lib/typed-event-emitter.js";
@@ -166,7 +167,7 @@ interface SessionConfig {
   logUrl?: string;
   sdkSessionId?: string;
   model?: string;
-  executionMode?: "plan" | "acceptEdits" | "default";
+  executionMode?: ExecutionMode;
   /** Additional directories Claude can access beyond cwd (for worktree support) */
   additionalDirectories?: string[];
 }

apps/twig/src/renderer/features/message-editor/components/DiffStatsIndicator.tsx

@@ -0,0 +1,60 @@
+import { Circle } from "@phosphor-icons/react";
+import { Flex, Text } from "@radix-ui/themes";
+import { trpcVanilla } from "@renderer/trpc";
+import { useQuery } from "@tanstack/react-query";
+
+interface DiffStatsIndicatorProps {
+  repoPath: string | null | undefined;
+}
+
+export function DiffStatsIndicator({ repoPath }: DiffStatsIndicatorProps) {
+  const { data: diffStats } = useQuery({
+    queryKey: ["diff-stats", repoPath],
+    queryFn: () =>
+      trpcVanilla.git.getDiffStats.query({
+        directoryPath: repoPath as string,
+      }),
+    enabled: !!repoPath,
+    staleTime: 5000,
+    refetchInterval: 5000,
+    placeholderData: (prev) => prev,
+  });
+
+  if (!diffStats || diffStats.filesChanged === 0) {
+    return null;
+  }
+
+  return (
+    <Flex align="center" gap="2">
+      <Circle size={4} weight="fill" color="var(--gray-9)" />
+      <Text
+        size="1"
+        style={{
+          color: "var(--gray-11)",
+          fontFamily: "monospace",
+        }}
+      >
+        {diffStats.filesChanged}{" "}
+        {diffStats.filesChanged === 1 ? "file" : "files"}
+      </Text>
+      <Text
+        size="1"
+        style={{
+          color: "var(--green-9)",
+          fontFamily: "monospace",
+        }}
+      >
+        +{diffStats.linesAdded}
+      </Text>
+      <Text
+        size="1"
+        style={{
+          color: "var(--red-9)",
+          fontFamily: "monospace",
+        }}
+      >
+        -{diffStats.linesRemoved}
+      </Text>
+    </Flex>
+  );
+}

apps/twig/src/renderer/features/message-editor/components/MessageEditor.tsx

@@ -10,6 +10,7 @@ import { useDraftStore } from "../stores/draftStore";
 import { useTiptapEditor } from "../tiptap/useTiptapEditor";
 import type { EditorHandle } from "../types";
 import type { EditorContent as EditorContentType } from "../utils/content";
+import { DiffStatsIndicator } from "./DiffStatsIndicator";
 import { EditorToolbar } from "./EditorToolbar";
 import { ModeIndicatorInput } from "./ModeIndicatorInput";
 
@@ -26,7 +27,7 @@ interface MessageEditorProps {
   onAttachFiles?: (files: File[]) => void;
   autoFocus?: boolean;
   currentMode?: ExecutionMode;
-  onModeChange?: () => void;
+  onModeChange?: (mode: ExecutionMode) => void;
 }
 
 export const MessageEditor = forwardRef<EditorHandle, MessageEditorProps>(
@@ -206,7 +207,13 @@ export const MessageEditor = forwardRef<EditorHandle, MessageEditorProps>(
           </Flex>
         </Flex>
         {onModeChange && currentMode && (
-          <ModeIndicatorInput mode={currentMode} taskId={taskId} />
+          <Flex align="center" gap="2">
+            <ModeIndicatorInput
+              mode={currentMode}
+              onModeChange={onModeChange}
+            />
+            <DiffStatsIndicator repoPath={repoPath} />
+          </Flex>
         )}
       </Flex>
     );