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/stats.rs

@@ -618,7 +618,7 @@ pub async fn save_stats(app: &tauri::AppHandle, stats: &UsageStats) -> Result<()
 
     let persisted = PersistedStats::from(stats);
 
-    println!("Saving stats: {:?}", persisted);
+    tracing::info!("Saving stats: {:?}", persisted);
 
     store.set(
         "lifetime_stats",
@@ -626,32 +626,32 @@ pub async fn save_stats(app: &tauri::AppHandle, stats: &UsageStats) -> Result<()
     );
     store.save().map_err(|e| e.to_string())?;
 
-    println!("Stats saved successfully");
+    tracing::info!("Stats saved successfully");
     Ok(())
 }
 
 /// Load lifetime stats from persistent store
 pub async fn load_stats(app: &tauri::AppHandle) -> Option<PersistedStats> {
-    println!("Loading stats from store...");
+    tracing::info!("Loading stats from store...");
 
     let store = match app.store("stats.json") {
         Ok(s) => s,
         Err(e) => {
-            println!("Failed to open stats store: {}", e);
+            tracing::error!("Failed to open stats store: {}", e);
             return None;
         }
     };
 
     if let Some(stats_value) = store.get("lifetime_stats") {
-        println!("Found lifetime stats in store: {:?}", stats_value);
+        tracing::info!("Found lifetime stats in store: {:?}", stats_value);
         if let Ok(persisted) = serde_json::from_value::<PersistedStats>(stats_value.clone()) {
-            println!("Loaded lifetime stats successfully");
+            tracing::info!("Loaded lifetime stats successfully");
             return Some(persisted);
         } else {
-            println!("Failed to parse lifetime stats");
+            tracing::error!("Failed to parse lifetime stats");
         }
     } else {
-        println!("No lifetime stats found in store");
+        tracing::info!("No lifetime stats found in store");
     }
 
     None