refactor(database): move db into typescript

- Implemented githubTokensDb for managing GitHub tokens with CRUD operations.
- Created
otificationPreferencesDb to handle user notification preferences.
- Added projectsDb for project path management and related operations.
- Introduced pushSubscriptionsDb for managing browser push subscriptions.
- Developed scanStateDb to track the last scanned timestamp.
- Established sessionsDb for session management with CRUD functionalities.
- Created userDb for user management, including authentication and onboarding.
- Implemented apidKeysDb for storing and managing VAPID keys.

feat(database): define schema for new database tables

- Added SQL schema definitions for users, API keys, user credentials, notification preferences, VAPID keys, push subscriptions, projects, sessions, scan state, and app configuration.
- Included necessary indexes for performance optimization.

refactor(shared): enhance type definitions and utility functions

- Updated shared types and interfaces for improved clarity and consistency.
- Added new types for credential management and provider-specific operations.
- Refined utility functions for better error handling and message normalization.

server/modules/database/repositories/notification-preferences.ts

@@ -0,0 +1,103 @@
+/**
+ * Notification preferences repository.
+ *
+ * Stores per-user notification channel/event preferences as JSON.
+ */
+
+import { getConnection } from '@/modules/database/connection.js';
+
+type NotificationPreferences = {
+  channels: {
+    inApp: boolean;
+    webPush: boolean;
+  };
+  events: {
+    actionRequired: boolean;
+    stop: boolean;
+    error: boolean;
+  };
+};
+
+const DEFAULT_NOTIFICATION_PREFERENCES: NotificationPreferences = {
+  channels: {
+    inApp: false,
+    webPush: false,
+  },
+  events: {
+    actionRequired: true,
+    stop: true,
+    error: true,
+  },
+};
+
+function normalizeNotificationPreferences(value: unknown): NotificationPreferences {
+  const source = value && typeof value === 'object' ? (value as Record<string, any>) : {};
+
+  return {
+    channels: {
+      inApp: source.channels?.inApp === true,
+      webPush: source.channels?.webPush === true,
+    },
+    events: {
+      actionRequired: source.events?.actionRequired !== false,
+      stop: source.events?.stop !== false,
+      error: source.events?.error !== false,
+    },
+  };
+}
+
+export const notificationPreferencesDb = {
+  /** Returns the normalized preferences for a user, creating defaults on first read. */
+  getNotificationPreferences(userId: number): NotificationPreferences {
+    const db = getConnection();
+    const row = db
+      .prepare(
+        'SELECT preferences_json FROM user_notification_preferences WHERE user_id = ?'
+      )
+      .get(userId) as { preferences_json: string } | undefined;
+
+    if (!row) {
+      const defaults = normalizeNotificationPreferences(DEFAULT_NOTIFICATION_PREFERENCES);
+      db.prepare(
+        'INSERT INTO user_notification_preferences (user_id, preferences_json, updated_at) VALUES (?, ?, CURRENT_TIMESTAMP)'
+      ).run(userId, JSON.stringify(defaults));
+      return defaults;
+    }
+
+    let parsed: unknown = DEFAULT_NOTIFICATION_PREFERENCES;
+    try {
+      parsed = JSON.parse(row.preferences_json);
+    } catch {
+      parsed = DEFAULT_NOTIFICATION_PREFERENCES;
+    }
+    return normalizeNotificationPreferences(parsed);
+  },
+
+  /** Upserts normalized preferences for a user and returns the stored value. */
+  updateNotificationPreferences(
+    userId: number,
+    preferences: unknown
+  ): NotificationPreferences {
+    const normalized = normalizeNotificationPreferences(preferences);
+    const db = getConnection();
+
+    db.prepare(
+      `INSERT INTO user_notification_preferences (user_id, preferences_json, updated_at)
+       VALUES (?, ?, CURRENT_TIMESTAMP)
+       ON CONFLICT(user_id) DO UPDATE SET
+         preferences_json = excluded.preferences_json,
+         updated_at = CURRENT_TIMESTAMP`
+    ).run(userId, JSON.stringify(normalized));
+
+    return normalized;
+  },
+
+  // Legacy aliases used by existing services/routes
+  getPreferences(userId: number): NotificationPreferences {
+    return notificationPreferencesDb.getNotificationPreferences(userId);
+  },
+  updatePreferences(userId: number, preferences: unknown): NotificationPreferences {
+    return notificationPreferencesDb.updateNotificationPreferences(userId, preferences);
+  },
+};
+