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/lib/stores/conversations.ts

@@ -28,7 +28,7 @@ export interface Conversation {
   characterState: CharacterState;
   isProcessing: boolean;
   grantedTools: Set<string>;
-  pendingPermission: PermissionRequest | null;
+  pendingPermissions: PermissionRequest[];
   pendingQuestion: UserQuestionEvent | null;
   scrollPosition: number;
   createdAt: Date;
@@ -66,7 +66,7 @@ function createConversationsStore() {
       characterState: "idle",
       isProcessing: false,
       grantedTools: new Set(),
-      pendingPermission: null,
+      pendingPermissions: [],
       pendingQuestion: null,
       scrollPosition: -1, // -1 means "scroll to bottom" (auto-scroll)
       createdAt: new Date(),
@@ -120,7 +120,11 @@ function createConversationsStore() {
   );
   const pendingPermission = derived(
     activeConversation,
-    ($conv) => $conv?.pendingPermission || null
+    ($conv) => $conv?.pendingPermissions[0] || null
+  );
+  const pendingPermissions = derived(
+    activeConversation,
+    ($conv) => $conv?.pendingPermissions || []
   );
   const pendingQuestion = derived(activeConversation, ($conv) => $conv?.pendingQuestion || null);
   const scrollPosition = derived(activeConversation, ($conv) => $conv?.scrollPosition ?? -1);
@@ -133,6 +137,7 @@ function createConversationsStore() {
     currentWorkingDirectory: { subscribe: currentWorkingDirectory.subscribe },
     terminalLines: { subscribe: terminalLines.subscribe },
     pendingPermission: { subscribe: pendingPermission.subscribe },
+    pendingPermissions: { subscribe: pendingPermissions.subscribe },
     pendingQuestion: { subscribe: pendingQuestion.subscribe },
     isProcessing: { subscribe: isProcessing.subscribe },
     grantedTools: { subscribe: grantedTools.subscribe },
@@ -190,7 +195,7 @@ function createConversationsStore() {
       conversations.update((convs) => {
         const conv = convs.get(activeId);
         if (conv) {
-          conv.pendingPermission = request;
+          conv.pendingPermissions.push(request);
           conv.lastActivityAt = new Date();
         }
         return convs;
@@ -203,7 +208,7 @@ function createConversationsStore() {
       conversations.update((convs) => {
         const conv = convs.get(activeId);
         if (conv) {
-          conv.pendingPermission = null;
+          conv.pendingPermissions = [];
           conv.lastActivityAt = new Date();
         }
         return convs;
@@ -213,7 +218,7 @@ function createConversationsStore() {
       conversations.update((convs) => {
         const conv = convs.get(conversationId);
         if (conv) {
-          conv.pendingPermission = request;
+          conv.pendingPermissions.push(request);
           conv.lastActivityAt = new Date();
         }
         return convs;
@@ -223,7 +228,30 @@ function createConversationsStore() {
       conversations.update((convs) => {
         const conv = convs.get(conversationId);
         if (conv) {
-          conv.pendingPermission = null;
+          conv.pendingPermissions = [];
+          conv.lastActivityAt = new Date();
+        }
+        return convs;
+      });
+    },
+    removePermission: (id: string) => {
+      const activeId = get(activeConversationId);
+      if (!activeId) return;
+
+      conversations.update((convs) => {
+        const conv = convs.get(activeId);
+        if (conv) {
+          conv.pendingPermissions = conv.pendingPermissions.filter((p) => p.id !== id);
+          conv.lastActivityAt = new Date();
+        }
+        return convs;
+      });
+    },
+    removePermissionForConversation: (conversationId: string, id: string) => {
+      conversations.update((convs) => {
+        const conv = convs.get(conversationId);
+        if (conv) {
+          conv.pendingPermissions = conv.pendingPermissions.filter((p) => p.id !== id);
           conv.lastActivityAt = new Date();
         }
         return convs;