To update your build system in an ongoing project, replace the package.json and gulpfile.js files with the new versions, then delete the node_modules folder and the package-lock.json files and run npm install from the command-line. You can also optionally delete the .babelrc file if it exists, as it is no longer used, but it won't hurt anything either way.
I recommend backing up your old version via a version control system (like GitHub or BitBucket) so that you can revert the changes if things go wrong. If you don't or can't and things do indeed go wrong, saving a copy of the old package.json and gulpfile.js files is enough for you to revert back using the same process outlined above.
You can check which version you currently are using and which version is the latest available in this repo in the package.json files, right up near the top.
Note: If you update to tweego-setup v2.0.0 or higher, you need to be sure to update to Tweego v2.0.0 or higher.