The packages that are built-in to Atom are designed to be in lockstep with Atom. So it is not recommended to attempt changing the version of a package that ships with Atom. If you want something newer than the Stable release, you can download the Beta release at https://atom.io/beta. If you want something newer still, you can follow the build instructions linked from the Atom README.
Warning: The Beta channel is intended for developers and early adopters. Building from source is only intended for developers. Use with caution.