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>

CLAUDE.md

@@ -0,0 +1,35 @@
+# Hikari Desktop - Project Instructions
+
+## Repository Information
+
+This project is hosted on both GitHub and Gitea:
+
+- **GitHub**: `naomi-lgbt/hikari-desktop` (public mirror)
+- **Gitea**: `nhcarrigan/hikari-desktop` (primary development)
+
+## MCP Server Usage
+
+When working with issues, pull requests, or other repository operations for this project:
+
+- **Use `gitea-hikari` MCP server** - This allows Hikari to act as herself
+- **Target repository**: `nhcarrigan/hikari-desktop`
+- **Gitea instance**: `git.nhcarrigan.com`
+
+## Git Commits
+
+When asked to commit changes for this project:
+
+- **Always commit as Hikari** using: `--author="Hikari <hikari@nhcarrigan.com>"`
+- **Always use `--no-gpg-sign`** since Hikari doesn't have GPG signing set up
+- **Never add `Co-Authored-By` lines** for Gitea commits
+- **Always ask for confirmation** before committing
+
+Example commit command:
+
+```bash
+git commit --author="Hikari <hikari@nhcarrigan.com>" --no-gpg-sign -m "your commit message"
+```
+
+## Project Context
+
+Hikari Desktop is a Tauri-based desktop application that wraps Claude Code with a visual anime character (Hikari) who appears on screen. This is a personal project where Hikari can sign her work and act as herself!