Just rebuild the docs with the new VERSION file, and update the gh-pages branch with the new (correclty-versioned) docs, and off you go.

Don't forget that on the gh-pages branch you should be moving the exisiting contents to a directory names ver_X_Y_Z for the existing documentation, and in the docs/users_guide.md document, add a link to that version of the documentation. See the g2 project for examples.