There are a couple of duplicate file finders for Linux listed e.g. here. I have already tried fdupes and fslint. However, from what I have seen, these will find all duplicates of the selected directory-structures/search paths and thus also duplicates that exist inside only one of the search-paths (if you select multiple).
However what I need/want is to search for duplicates against a reference path, where I can define one path to be the reference path, and search inside the other path, for files that exist in the reference path in order to remove them.
I need to do this, to prepare two large directory-structure that have gotten out of sync, where one is more up-to-date than the other (this would be my reference). Most of the files should be duplicates between the two, but I suspect, that there are still some files only on the other path, so that I don't want to just remove it.
Are there perhaps some options to fdupes to achieve this, that I have overlooked?
I have tried writing a Python script to clean up the list that fdupes outputs, but not with success.