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/components/StatusBar.svelte

@@ -33,6 +33,7 @@
     sanitizeForJson,
   } from "$lib/utils/conversationUtils";
   import { updateDiscordRpc, setSkipNextGreeting } from "$lib/tauri";
+  import { debugConsoleStore } from "$lib/stores/debugConsole";
 
   const DISCORD_URL = "https://chat.nhcarrigan.com";
   const DONATE_URL = "https://donate.nhcarrigan.com";
@@ -69,7 +70,6 @@
     update_checks_enabled: true,
     character_panel_width: null,
     font_size: 14,
-    minimize_to_tray: false,
     streamer_mode: false,
     streamer_hide_paths: false,
     compact_mode: false,
@@ -507,6 +507,20 @@
         />
       </svg>
     </button>
+    <button
+      onclick={() => debugConsoleStore.toggle()}
+      class="p-1 text-gray-500 icon-trans-hover"
+      title="Debug Console (Ctrl+`)"
+    >
+      <svg class="w-5 h-5" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+        <path
+          stroke-linecap="round"
+          stroke-linejoin="round"
+          stroke-width="2"
+          d="M8 9l3 3-3 3m5 0h3M5 20h14a2 2 0 002-2V6a2 2 0 00-2-2H5a2 2 0 00-2 2v12a2 2 0 002 2z"
+        />
+      </svg>
+    </button>
     <button
       onclick={configStore.openSidebar}
       class="p-1 text-gray-500 icon-trans-hover"