Hi, to add to this idea, it would be nice to be able completely lock one path against modification, basically using it as a stable reference.
I think that one scenario that often comes up is that your goal is not to eliminate all duplicates. Rather, you want to 'validate' one directory structure against another. This comes up when you manually back up or reorganize files from one location to another, and then want to verify that the target contains all the files from the source before deleting them.
To make this more concrete, I collect all the photos from the various family phones and manually sort them into a folder structure. Inside that structure, I sometimes create albums with intentional duplicates, so I do not really care about internal duplication there. I leave the photos on the phones though, so it is not immediately obvious which photos are already in the sorted structure. When I need to delete photos from the phones to make space, I want to ensure that all photos that I delete have been copied into the sorted structure. By marking the sorted structure as locked or 'for reference', I could easily delete all sorted photos from a phone, without accidentally deleting my albums within the sorted structure.
There is an old discussion thread where people have the same requirement. The third party tool mentioned there offers such a locking mechanism, which is a really elegant and simple solution to the problem.
As a second point, I don't really use copies, but hard link clones for my albums. The find duplicates function does not distinguish between true copies and hard links to the same file. It would be nice to have that ability as an optional behavior, i.e. 'Ignore hard links' or 'do not flag hard links as duplicates'.