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/github-tokens.ts

@@ -0,0 +1,100 @@
+/**
+ * GitHub tokens repository.
+ *
+ * Backward-compatible helper layer over generic credentials storage.
+ * Tokens are stored in `user_credentials` with `credential_type = 'github_token'`.
+ */
+
+import { getConnection } from '@/modules/database/connection.js';
+import { credentialsDb } from '@/modules/database/repositories/credentials.js';
+import type {
+  CredentialPublicRow,
+  CreateCredentialResult,
+} from '@/shared/types.js';
+
+const GITHUB_TOKEN_TYPE = 'github_token';
+
+type CredentialRow = {
+  id: number;
+  user_id: number;
+  credential_name: string;
+  credential_type: string;
+  credential_value: string;
+  description: string | null;
+  created_at: string;
+  is_active: number;
+};
+
+type GithubTokenLookup = CredentialRow & {
+  github_token: string;
+};
+
+export const githubTokensDb = {
+  /** Creates a GitHub token credential entry. */
+  createGithubToken(
+    userId: number,
+    tokenName: string,
+    githubToken: string,
+    description: string | null = null
+  ): CreateCredentialResult {
+    return credentialsDb.createCredential(
+      userId,
+      tokenName,
+      GITHUB_TOKEN_TYPE,
+      githubToken,
+      description
+    );
+  },
+
+  /** Returns all GitHub tokens (safe shape: no credential value). */
+  getGithubTokens(userId: number): CredentialPublicRow[] {
+    return credentialsDb.getCredentials(userId, GITHUB_TOKEN_TYPE);
+  },
+
+  /** Returns the most recent active GitHub token value for a user. */
+  getActiveGithubToken(userId: number): string | null {
+    return credentialsDb.getActiveCredential(userId, GITHUB_TOKEN_TYPE);
+  },
+
+  /**
+   * Returns a specific active GitHub token row by id/user, including
+   * a `github_token` compatibility field.
+   */
+  getGithubTokenById(userId: number, tokenId: number): GithubTokenLookup | null {
+    const db = getConnection();
+    const row = db
+      .prepare(
+        `SELECT *
+         FROM user_credentials
+         WHERE id = ? AND user_id = ? AND credential_type = ? AND is_active = 1`
+      )
+      .get(tokenId, userId, GITHUB_TOKEN_TYPE) as CredentialRow | undefined;
+
+    if (!row) return null;
+
+    return {
+      ...row,
+      github_token: row.credential_value,
+    };
+  },
+
+  /** Updates active state for a GitHub token. */
+  updateGithubToken(
+    userId: number,
+    tokenId: number,
+    isActive: boolean
+  ): boolean {
+    return credentialsDb.toggleCredential(userId, tokenId, isActive);
+  },
+
+  /** Deletes a GitHub token. */
+  deleteGithubToken(userId: number, tokenId: number): boolean {
+    return credentialsDb.deleteCredential(userId, tokenId);
+  },
+
+  // Legacy alias used by existing routes
+  toggleGithubToken(userId: number, tokenId: number, isActive: boolean): boolean {
+    return githubTokensDb.updateGithubToken(userId, tokenId, isActive);
+  },
+};
+