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/debugConsole.ts

@@ -0,0 +1,154 @@
+import { writable, derived } from "svelte/store";
+import { listen } from "@tauri-apps/api/event";
+
+export type LogLevel = "debug" | "info" | "warn" | "error";
+
+export interface LogEntry {
+  id: string;
+  timestamp: Date;
+  level: LogLevel;
+  message: string;
+  source: "frontend" | "backend";
+}
+
+interface DebugConsoleState {
+  logs: LogEntry[];
+  isOpen: boolean;
+  maxLogs: number;
+  filterLevel: LogLevel | "all";
+  autoScroll: boolean;
+}
+
+const MAX_LOGS = 1000; // Circular buffer size
+
+function createDebugConsoleStore() {
+  const { subscribe, update } = writable<DebugConsoleState>({
+    logs: [],
+    isOpen: false,
+    maxLogs: MAX_LOGS,
+    filterLevel: "all",
+    autoScroll: true,
+  });
+
+  let logCounter = 0;
+
+  function addLog(level: LogLevel, message: string, source: "frontend" | "backend") {
+    update((state) => {
+      const newLog: LogEntry = {
+        id: `log-${Date.now()}-${logCounter++}`,
+        timestamp: new Date(),
+        level,
+        message,
+        source,
+      };
+
+      const updatedLogs = [...state.logs, newLog];
+
+      // Implement circular buffer - remove oldest if exceeding max
+      if (updatedLogs.length > state.maxLogs) {
+        updatedLogs.shift();
+      }
+
+      return { ...state, logs: updatedLogs };
+    });
+  }
+
+  // Override console methods to capture frontend logs
+  const originalConsole = {
+    log: console.log,
+    info: console.info,
+    warn: console.warn,
+    error: console.error,
+    debug: console.debug,
+  };
+
+  function setupConsoleCapture() {
+    console.log = (...args: unknown[]) => {
+      originalConsole.log(...args);
+      addLog("info", args.map((arg) => String(arg)).join(" "), "frontend");
+    };
+
+    console.info = (...args: unknown[]) => {
+      originalConsole.info(...args);
+      addLog("info", args.map((arg) => String(arg)).join(" "), "frontend");
+    };
+
+    console.warn = (...args: unknown[]) => {
+      originalConsole.warn(...args);
+      addLog("warn", args.map((arg) => String(arg)).join(" "), "frontend");
+    };
+
+    console.error = (...args: unknown[]) => {
+      originalConsole.error(...args);
+      addLog("error", args.map((arg) => String(arg)).join(" "), "frontend");
+    };
+
+    console.debug = (...args: unknown[]) => {
+      originalConsole.debug(...args);
+      addLog("debug", args.map((arg) => String(arg)).join(" "), "frontend");
+    };
+
+    // Capture unhandled errors
+    window.addEventListener("error", (event) => {
+      addLog(
+        "error",
+        `[Unhandled Error] ${event.message} at ${event.filename}:${event.lineno}:${event.colno}`,
+        "frontend"
+      );
+    });
+
+    // Capture unhandled promise rejections
+    window.addEventListener("unhandledrejection", (event) => {
+      addLog("error", `[Unhandled Promise Rejection] ${event.reason}`, "frontend");
+    });
+  }
+
+  function restoreConsole() {
+    console.log = originalConsole.log;
+    console.info = originalConsole.info;
+    console.warn = originalConsole.warn;
+    console.error = originalConsole.error;
+    console.debug = originalConsole.debug;
+  }
+
+  // Listen for backend logs
+  async function setupBackendLogsListener() {
+    await listen<{ level: LogLevel; message: string }>("debug:log", (event) => {
+      addLog(event.payload.level, event.payload.message, "backend");
+    });
+  }
+
+  return {
+    subscribe,
+    toggle: () => update((state) => ({ ...state, isOpen: !state.isOpen })),
+    open: () => update((state) => ({ ...state, isOpen: true })),
+    close: () => update((state) => ({ ...state, isOpen: false })),
+    clear: () => update((state) => ({ ...state, logs: [] })),
+    setFilterLevel: (level: LogLevel | "all") =>
+      update((state) => ({ ...state, filterLevel: level })),
+    setAutoScroll: (enabled: boolean) => update((state) => ({ ...state, autoScroll: enabled })),
+    setupConsoleCapture,
+    restoreConsole,
+    setupBackendLogsListener,
+  };
+}
+
+export const debugConsoleStore = createDebugConsoleStore();
+
+// Derived store for filtered logs
+export const filteredLogs = derived(debugConsoleStore, ($debugConsole) => {
+  if ($debugConsole.filterLevel === "all") {
+    return $debugConsole.logs;
+  }
+
+  const levelPriority: Record<LogLevel, number> = {
+    debug: 0,
+    info: 1,
+    warn: 2,
+    error: 3,
+  };
+
+  const minPriority = levelPriority[$debugConsole.filterLevel];
+
+  return $debugConsole.logs.filter((log) => levelPriority[log.level] >= minPriority);
+});