@Inject JavaIoFileSystemAccess javaFsa

void doGenerate(Resource model, IFileSystemAccess2 fsa, IGeneratorContext context) {
    // ...

    // successfully deletes the specified file when using the language server,
    // but not when using the eclipse-runtime instance.
    javaFsa.deleteFile(filepath); 

    // Prevent language server from calling fsa.deleteFile to prevent UnsupportedOperationException.
    if(fsa.isFile(filepath) { 
        // While this is never called by the language server, the eclipse instance doesn't call it either...
        fsa.deleteFile(filepath); 
    }
   // ...
}