The plugin is built using Webpack, which creates the compiled code in `/dist`. A JPL archive will also be created at the root, which can use to distribute the plugin.
In general this command tries to do the right thing - in particular it's going to merge the changes in package.json and .gitignore instead of overwriting. It will also leave "/src" as well as README.md untouched.
The file that may cause problem is "webpack.config.js" because it's going to be overwritten. For that reason, if you want to change it, consider creating a separate JavaScript file and include it in webpack.config.js. That way, when you update, you only have to restore the line that include your file.