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/debug_logger.rs

@@ -0,0 +1,78 @@
+use serde::{Deserialize, Serialize};
+use std::sync::Arc;
+use tauri::{AppHandle, Emitter};
+use tracing::{Level, Subscriber};
+use tracing_subscriber::layer::{Context, Layer};
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct DebugLogEvent {
+    pub level: String,
+    pub message: String,
+}
+
+#[derive(Clone)]
+pub struct TauriLogLayer {
+    app: Arc<AppHandle>,
+}
+
+impl TauriLogLayer {
+    pub fn new(app: AppHandle) -> Self {
+        Self {
+            app: Arc::new(app),
+        }
+    }
+}
+
+impl<S> Layer<S> for TauriLogLayer
+where
+    S: Subscriber,
+{
+    fn on_event(
+        &self,
+        event: &tracing::Event<'_>,
+        _ctx: Context<'_, S>,
+    ) {
+        let metadata = event.metadata();
+        let level = match *metadata.level() {
+            Level::ERROR => "error",
+            Level::WARN => "warn",
+            Level::INFO => "info",
+            Level::DEBUG => "debug",
+            Level::TRACE => "debug",
+        };
+
+        // Extract message from the event
+        struct MessageVisitor {
+            message: String,
+        }
+
+        impl tracing::field::Visit for MessageVisitor {
+            fn record_debug(&mut self, field: &tracing::field::Field, value: &dyn std::fmt::Debug) {
+                if field.name() == "message" {
+                    self.message = format!("{:?}", value);
+                }
+            }
+        }
+
+        let mut visitor = MessageVisitor {
+            message: String::new(),
+        };
+        event.record(&mut visitor);
+
+        // If we couldn't extract a message, try to format the whole event
+        if visitor.message.is_empty() {
+            visitor.message = metadata.name().to_string();
+        }
+
+        // Strip quotes from the message
+        let message = visitor.message.trim_matches('"').to_string();
+
+        let log_event = DebugLogEvent {
+            level: level.to_string(),
+            message,
+        };
+
+        // Emit to frontend
+        let _ = self.app.emit("debug:log", log_event);
+    }
+}