For anime AniDB has several applications that automatically mark episodes as watched. Personally I mark them manually so I can't help you with this except for providing some links:
- https://anidb.net/software list of software
- https://wiki.anidb.net you might find something relevant on the wiki
- #[email protected] main IRC channel for help/chatting
Sorry that I can't be of much help but I don't use anime-dl so it would be hard for me to provide any reliable info. But AniDB doesn't provide any links to watching anime (except for a few licensed platforms) so it probably won't be of much help when searching for download links. But if you download files from groups (which seems to be the case looking at your example with [Judas]), AniDB does have file checksums for many groups so you can mark episodes as watched and query anime info basing on it. I'm unable to give any specifics though, sorry.