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/routes/+page.svelte

@@ -1,6 +1,7 @@
 <script lang="ts">
   import { onMount, onDestroy } from "svelte";
   import { invoke } from "@tauri-apps/api/core";
+  import { listen } from "@tauri-apps/api/event";
   import { get } from "svelte/store";
   import {
     initializeTauriListeners,
@@ -31,12 +32,16 @@
   import AchievementNotification from "$lib/components/AchievementNotification.svelte";
   import AchievementsPanel from "$lib/components/AchievementsPanel.svelte";
   import UpdateNotification from "$lib/components/UpdateNotification.svelte";
+  import CloseAppConfirmModal from "$lib/components/CloseAppConfirmModal.svelte";
+  import { debugConsoleStore } from "$lib/stores/debugConsole";
 
   let initialized = false;
   let updateNotification: UpdateNotification | undefined = $state(undefined);
   let achievementPanelOpen = $state(false);
   let currentCharacterState: CharacterState = $state("idle");
   let compactModeActive = $state(false);
+  let closeConfirmModalOpen = $state(false);
+  let hasActiveConversation = $state(false);
 
   // Editor state
   const isEditorVisible = editorStore.isEditorVisible;
@@ -230,6 +235,13 @@
       return;
     }
 
+    // Ctrl+` - Toggle debug console
+    if (event.ctrlKey && event.key === "`") {
+      event.preventDefault();
+      debugConsoleStore.toggle();
+      return;
+    }
+
     // Ctrl+E - Toggle editor panel (only when connected)
     if (event.ctrlKey && event.key === "e") {
       event.preventDefault();
@@ -342,6 +354,50 @@
     }
   }
 
+  async function handleCloseRequest() {
+    // Check if there's an active conversation with Claude running
+    const activeId = get(claudeStore.activeConversationId);
+    if (activeId) {
+      try {
+        const isRunning = await invoke<boolean>("is_claude_running", {
+          conversationId: activeId,
+        });
+        hasActiveConversation = isRunning;
+      } catch (error) {
+        console.error("Failed to check Claude status:", error);
+        hasActiveConversation = false;
+      }
+    } else {
+      hasActiveConversation = false;
+    }
+
+    // Always show confirmation modal
+    closeConfirmModalOpen = true;
+  }
+
+  async function handleConfirmClose() {
+    closeConfirmModalOpen = false;
+    try {
+      await invoke("close_application");
+    } catch (error) {
+      console.error("Failed to close application:", error);
+    }
+  }
+
+  async function handleMinimizeToTray() {
+    closeConfirmModalOpen = false;
+    try {
+      const window = getCurrentWindow();
+      await window.hide();
+    } catch (error) {
+      console.error("Failed to minimize to tray:", error);
+    }
+  }
+
+  function handleCancelClose() {
+    closeConfirmModalOpen = false;
+  }
+
   onMount(async () => {
     if (!initialized) {
       initialized = true;
@@ -387,6 +443,16 @@
 
       // Initialize Discord RPC
       await initializeDiscordRpc();
+
+      // Listen for window close requests
+      const unlisten = await listen("window-close-requested", () => {
+        handleCloseRequest();
+      });
+
+      // Store the unlisten function for cleanup
+      window.addEventListener("beforeunload", () => {
+        unlisten();
+      });
     }
   });
 
@@ -453,6 +519,13 @@
       onClose={() => (achievementPanelOpen = false)}
     />
     <UpdateNotification bind:this={updateNotification} />
+    <CloseAppConfirmModal
+      isOpen={closeConfirmModalOpen}
+      {hasActiveConversation}
+      onClose={handleConfirmClose}
+      onMinimize={handleMinimizeToTray}
+      onCancel={handleCancelClose}
+    />
   </div>
 {/if}