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/achievements.rs

@@ -1671,7 +1671,7 @@ pub fn check_message_achievements(
     let mut newly_unlocked = Vec::new();
     let message_lower = message.to_lowercase();
 
-    println!("Checking message achievements for: {}", message);
+    tracing::info!("Checking message achievements for: {}", message);
 
     // Relationship & Greetings
     if message_lower.contains("good morning") && progress.unlock(AchievementId::GoodMorning) {
@@ -1863,18 +1863,18 @@ pub fn check_achievements(
 ) -> Vec<AchievementId> {
     let mut newly_unlocked = Vec::new();
 
-    println!(
+    tracing::info!(
         "Checking achievements with stats: messages={}, tokens={}, code_blocks={}",
         stats.messages_exchanged,
         stats.total_input_tokens + stats.total_output_tokens,
         stats.code_blocks_generated
     );
-    println!("Currently unlocked: {:?}", progress.unlocked);
+    tracing::info!("Currently unlocked: {:?}", progress.unlocked);
 
     // Token milestones
     let total_tokens = stats.total_input_tokens + stats.total_output_tokens;
     if total_tokens >= 1_000 && progress.unlock(AchievementId::FirstSteps) {
-        println!("Unlocked FirstSteps achievement!");
+        tracing::info!("Unlocked FirstSteps achievement!");
         newly_unlocked.push(AchievementId::FirstSteps);
     }
     if total_tokens >= 10_000 && progress.unlock(AchievementId::GrowingStrong) {
@@ -2244,7 +2244,7 @@ pub async fn save_achievements(
     // Create a serializable version with just the unlocked achievement IDs
     let unlocked_list: Vec<AchievementId> = progress.unlocked.iter().cloned().collect();
 
-    println!("Saving achievements: {:?}", unlocked_list);
+    tracing::info!("Saving achievements: {:?}", unlocked_list);
 
     store.set(
         "unlocked",
@@ -2252,18 +2252,18 @@ pub async fn save_achievements(
     );
     store.save().map_err(|e| e.to_string())?;
 
-    println!("Achievements saved successfully");
+    tracing::info!("Achievements saved successfully");
     Ok(())
 }
 
 // Load achievements from persistent store
 pub async fn load_achievements(app: &tauri::AppHandle) -> AchievementProgress {
-    println!("Loading achievements from store...");
+    tracing::info!("Loading achievements from store...");
 
     let store = match app.store("achievements.json") {
         Ok(s) => s,
         Err(e) => {
-            println!("Failed to open achievements store: {}", e);
+            tracing::error!("Failed to open achievements store: {}", e);
             return AchievementProgress::new();
         }
     };
@@ -2272,19 +2272,19 @@ pub async fn load_achievements(app: &tauri::AppHandle) -> AchievementProgress {
 
     // Get unlocked achievements
     if let Some(unlocked_value) = store.get("unlocked") {
-        println!("Found unlocked value in store: {:?}", unlocked_value);
+        tracing::info!("Found unlocked value in store: {:?}", unlocked_value);
         if let Ok(unlocked_list) =
             serde_json::from_value::<Vec<AchievementId>>(unlocked_value.clone())
         {
-            println!("Loaded {} achievements", unlocked_list.len());
+            tracing::info!("Loaded {} achievements", unlocked_list.len());
             for achievement_id in unlocked_list {
                 progress.unlocked.insert(achievement_id);
             }
         } else {
-            println!("Failed to parse unlocked achievements");
+            tracing::error!("Failed to parse unlocked achievements");
         }
     } else {
-        println!("No unlocked achievements found in store");
+        tracing::info!("No unlocked achievements found in store");
     }
 
     progress