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/lib.rs

@@ -4,6 +4,7 @@ mod clipboard;
 mod commands;
 mod config;
 mod cost_tracking;
+mod debug_logger;
 mod discord_rpc;
 mod git;
 mod notifications;
@@ -24,6 +25,7 @@ use bridge_manager::create_shared_bridge_manager;
 use clipboard::*;
 use commands::load_saved_achievements;
 use commands::*;
+use debug_logger::TauriLogLayer;
 use discord_rpc::DiscordRpcManager;
 use git::*;
 use notifications::*;
@@ -31,9 +33,11 @@ use quick_actions::*;
 use sessions::*;
 use snippets::*;
 use std::sync::Arc;
-use tauri::Manager;
+use tauri::{Emitter, Manager};
 use temp_manager::create_shared_temp_manager;
-use tray::{setup_tray, should_minimize_to_tray};
+use tracing_subscriber::layer::SubscriberExt;
+use tracing_subscriber::util::SubscriberInitExt;
+use tray::setup_tray;
 use vbs_notification::*;
 use windows_toast::*;
 use wsl_notifications::*;
@@ -58,6 +62,14 @@ pub fn run() {
         .manage(temp_manager.clone())
         .manage(discord_rpc.clone())
         .setup(move |app| {
+            // Initialize tracing with custom layer that emits to frontend
+            // NOTE: We don't use fmt::layer() because in production builds with windows_subsystem = "windows",
+            // stdout is hidden. Instead, all logs go through TauriLogLayer to the debug console.
+            let tauri_layer = TauriLogLayer::new(app.handle().clone());
+            tracing_subscriber::registry()
+                .with(tauri_layer)
+                .init();
+
             // Initialize the app handle in the bridge manager
             bridge_manager.lock().set_app_handle(app.handle().clone());
 
@@ -67,26 +79,29 @@ pub fn run() {
             // Clean up any orphaned temp files from previous sessions
             if let Ok(count) = temp_manager.lock().cleanup_orphaned_files() {
                 if count > 0 {
-                    println!("Cleaned up {} orphaned temp files", count);
+                    tracing::info!("Cleaned up {} orphaned temp files", count);
                 }
             }
 
+            tracing::info!("Hikari Desktop started successfully");
+
             // Set up system tray
             if let Err(e) = setup_tray(app.handle()) {
-                eprintln!("Failed to set up system tray: {}", e);
+                tracing::error!("Failed to set up system tray: {}", e);
             }
 
-            // Handle window close event for minimize to tray
+            // Handle window close event for minimize to tray and close confirmation
             let main_window = app.get_webview_window("main").unwrap();
             main_window.on_window_event({
                 let app_handle = app.handle().clone();
                 move |event| {
                     if let tauri::WindowEvent::CloseRequested { api, .. } = event {
-                        if should_minimize_to_tray(&app_handle) {
-                            api.prevent_close();
-                            if let Some(window) = app_handle.get_webview_window("main") {
-                                let _ = window.hide();
-                            }
+                        // Always prevent default close - let frontend handle it
+                        api.prevent_close();
+
+                        // Emit event to frontend to show confirmation modal
+                        if let Some(window) = app_handle.get_webview_window("main") {
+                            let _ = window.emit("window-close-requested", ());
                         }
                     }
                 }
@@ -181,6 +196,7 @@ pub fn run() {
             update_discord_rpc,
             stop_discord_rpc,
             log_discord_rpc,
+            close_application,
         ])
         .run(tauri::generate_context!())
         .expect("error while running tauri application");