You may edit all files except resources\application.properties as this could result in errors. File resources\application-eira.properties contains configuration that you may want to adapt such as main XSDs and XSLTs as well as texts and labels.
To publish changes commit and push your updates. In 1-2 minutes the online service will be updated.
The online service is accessible at https://www.itb.ec.europa.eu/eira/upload and the web service API at https://www.itb.ec.europa.eu/eira/api.