Hi,
I understood your requirement, you require file organizer tool, which can help finding duplicate files and allow user to make choice whether to retain, update or skip file.
Also, you want data to be updated in DB so that an index kind of stuff can be created, which help in longer run to find all duplicates and show to user.
I just want to know, which DB you want for it, H2, Mysql, Oracle etc...
Looking forward to discussing the same with you.