Once upon a time, we had a more complicated boot script that among other things handled the intermediate dialects of Newspeak and loading the icons from files. This version of nsboot lived in another repository whose URL I can't find after some quick searching of my inbox.
Today the icons come from the array literals in the methods of HopscotchImages, which are what used to be generated from the files.
In a future where we implement proper namespaces for the IDE, they will be versioned objects that live in the same repository as the class declarations.