When publishing a customization project, you might see some item being skipped for the reason of being already applied. Ex:
EntityEndpoint EntityEndpoint#6.00.001§DefaultPlus(skipped, already applied)
This can happen for any items contained saved in the database. Ex: Generic inquiries, reports, site map nodes, DB scripts, system locales, import/export scenarios, shared filters, access rights, wikis, web service endpoints and analytical reports.