You index it with btrees just like everything else. You distinguish it by configuring which folders to watch. You react to events with inotify. You don't give your music app write permission to your library. It only needs to write its indexes and playlists. All of your other questions become irrelevant; you delete the files you mean to delete with your file manager. In practice, music is small and storage is cheap, so deleting seems like a weird use-case for an application dedicated to music. I still have files that have been migrating across computers for 25 years.