Upgrade geopackage

[restjohn]

This PR upgrades the @ngageoint/geopackage dependency to the latest 4.2.8 so @ngageoint/mage.service installation can pull native binaries for better-sqlite3 in Node 24, which is required for GeoPackage functionality.

Additional Changes

All changes are in the service package.

• Fix null reference bug in an older database migration.
• Upgrade mongodb-memory-server dev dependency.
• Remove deprecated mongodb-memory-server configuration from package.json to silence NPM warnings. The MongoDB binary version is now in mongo.test.ts or env var MONGOMS_VERSION.
• Remove obsolete type definitions for @ngageoint/mongodb-migrations package which provides its own type definitions now.