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-tauri/src/tray.rs

@@ -4,8 +4,6 @@ use tauri::{
     AppHandle, Manager,
 };
 
-use crate::config::HikariConfig;
-
 pub fn setup_tray(app: &AppHandle) -> tauri::Result<()> {
     let show_item = MenuItem::with_id(app, "show", "Show Hikari", true, None::<&str>)?;
     let quit_item = MenuItem::with_id(app, "quit", "Quit", true, None::<&str>)?;
@@ -48,21 +46,3 @@ pub fn setup_tray(app: &AppHandle) -> tauri::Result<()> {
 
     Ok(())
 }
-
-pub fn should_minimize_to_tray(app: &AppHandle) -> bool {
-    let config_path = app
-        .path()
-        .app_config_dir()
-        .ok()
-        .map(|p| p.join("hikari-config.json"));
-
-    if let Some(path) = config_path {
-        if let Ok(content) = std::fs::read_to_string(&path) {
-            if let Ok(config) = serde_json::from_str::<HikariConfig>(&content) {
-                return config.minimize_to_tray;
-            }
-        }
-    }
-
-    false
-}