refactor: restructure db logic and add import alias using tsc-alias

Note: the legacy githubTokensDb migration is not included in this commit.
It's used only in `agents.js` and will be removed in a future commit. We
will directly use credentials repository instead of github tokens repository.

server/src/shared/database/migrations.ts

@@ -0,0 +1,44 @@
+import { Database } from "better-sqlite3";
+import { APP_CONFIG_TABLE_SCHEMA_SQL, SESSION_NAMES_TABLE_SCHEMA_SQL } from "@/shared/database/schema.js";
+import { logger } from "@/shared/utils/logger.js";
+
+const addColumnToUsersTableIfNotExists = (
+    db: Database,
+    columnNames: string[],
+    columnName: string,
+    columnType: string,
+) => {
+    if (!columnNames.includes(columnName)) {
+        logger.info(
+            `Running migration: Adding ${columnName} column to users table`,
+        );
+        db.exec(`ALTER TABLE users ADD COLUMN ${columnName} ${columnType}`);
+    }
+};
+
+export const runMigrations = (db: Database) => {
+    try {
+        const tableInfo = db.prepare("PRAGMA table_info(users)").all() as { name: string }[];
+        const columnNames = tableInfo.map((col) => col.name);
+
+        addColumnToUsersTableIfNotExists(db, columnNames, "git_name", "TEXT");
+        addColumnToUsersTableIfNotExists(db, columnNames, "git_email", "TEXT");
+        addColumnToUsersTableIfNotExists(db, columnNames, "has_completed_onboarding", "BOOLEAN DEFAULT 0",
+        );
+
+        // Create app_config table if it doesn't exist (for existing installations)
+        db.exec(APP_CONFIG_TABLE_SCHEMA_SQL);
+
+        // Create session_names table if it doesn't exist (for existing installations)
+        db.exec(SESSION_NAMES_TABLE_SCHEMA_SQL);
+        db.exec(
+            "CREATE INDEX IF NOT EXISTS idx_session_names_lookup ON session_names(session_id, provider)",
+        );
+
+        logger.info("Database migrations completed successfully");
+
+    } catch (error: any) {
+        logger.error("Error running migrations: ", error.message);
+        throw error;
+    }
+};