fix: critical permission modal and config issues (#127)

## Summary

This PR resolves several critical bugs that were blocking the permission modal and causing config loss:

- **Permission modal not appearing** - Fixed z-index issues and runtime errors
- **Config store race condition** - Resolved critical race condition causing settings to be lost
- **Excessive logging** - Removed redundant fmt layer that was writing to hidden stdout
- **System tool prompts** - Prevented unnecessary permission prompts for built-in tools
- **Permission batching** - Added support for parallel permission requests
- **ExitPlanMode tool** - Fixed ExitPlanMode tool not functioning correctly

## Changes Made

### Permission Modal Fixes
- Updated z-index to proper value (9999) to ensure modal appears above all other UI elements
- Fixed runtime errors that were preventing modal from rendering
- Resolved issues with permission grants not being properly applied

### Config Store Race Condition
- Fixed critical race condition where multiple rapid config updates would result in lost settings
- Ensured config writes are properly sequenced to prevent data loss
- Added proper synchronisation for config store operations

### Logging Cleanup
- Removed redundant fmt formatting layer that was outputting to hidden stdout
- Cleaned up excessive debug logging added during troubleshooting
- Removed temporary debugging documentation files

### UX Improvements
- Added close confirmation modal with minimise to tray option
- Implemented batching for parallel permission requests
- Added debug console for viewing frontend and backend logs

### ExitPlanMode Fix
- Fixed ExitPlanMode tool not functioning correctly, ensuring proper transitions out of plan mode

## Issues Resolved

Closes #112 - Permission flow now properly handles multiple tool requests
Closes #113 - ExitPlanMode tool now functions correctly
Closes #126 - Debug console feature added (partial - basic implementation complete)

## Test Plan

- [x] Permission modal appears and functions correctly
- [x] Config settings persist across app restarts
- [x] No excessive logging in production builds
- [x] System tools don't trigger permission prompts
- [x] Parallel permission requests are properly batched
- [x] Debug console displays frontend and backend logs
- [x] ExitPlanMode properly exits plan mode

---
✨ This PR was created with help from Hikari~ 🌸

Co-authored-by: Naomi Carrigan <commits@nhcarrigan.com>
Reviewed-on: #127
Co-authored-by: Hikari <hikari@nhcarrigan.com>
Co-committed-by: Hikari <hikari@nhcarrigan.com>

src/lib/tauri.ts

@@ -328,31 +328,41 @@ export async function initializeTauriListeners() {
   });
   unlisteners.push(cwdUnlisten);
 
+  console.log("[Tauri Listener] Setting up claude:permission listener");
   const permissionUnlisten = await listen<PermissionPromptEvent>("claude:permission", (event) => {
-    const { id, tool_name, tool_input, description, conversation_id } = event.payload;
+    const { permissions, conversation_id } = event.payload;
 
-    // Store permission request for the specific conversation
-    if (conversation_id) {
-      claudeStore.requestPermissionForConversation(conversation_id, {
-        id,
-        tool: tool_name,
-        description,
-        input: tool_input,
-      });
-      claudeStore.addLineToConversation(
-        conversation_id,
-        "system",
-        `Permission requested for: ${tool_name}`
-      );
-    } else {
-      // Fallback to active conversation if no conversation_id
-      claudeStore.requestPermission({
-        id,
-        tool: tool_name,
-        description,
-        input: tool_input,
-      });
-      claudeStore.addLine("system", `Permission requested for: ${tool_name}`);
+    console.log(
+      `[Permission] Event received: ${permissions.length} permission(s) for conversation ${conversation_id || "active"}`,
+      { permissions, conversation_id }
+    );
+
+    // Store each permission request for the specific conversation
+    for (const permission of permissions) {
+      const { id, tool_name, tool_input, description } = permission;
+
+      if (conversation_id) {
+        claudeStore.requestPermissionForConversation(conversation_id, {
+          id,
+          tool: tool_name,
+          description,
+          input: tool_input,
+        });
+        claudeStore.addLineToConversation(
+          conversation_id,
+          "system",
+          `Permission requested for: ${tool_name}`
+        );
+      } else {
+        // Fallback to active conversation if no conversation_id
+        claudeStore.requestPermission({
+          id,
+          tool: tool_name,
+          description,
+          input: tool_input,
+        });
+        claudeStore.addLine("system", `Permission requested for: ${tool_name}`);
+      }
     }
   });
   unlisteners.push(permissionUnlisten);