Need some way to deal with composite file-like folders on MacOS such as Logic Pro save files or .rtfd files

[kupietools]

Is your feature request related to a problem? Please describe.
Logic Pro documents resemble files but they are folders. The problem is, sometimes duplicates are necessary within them. For instance, if I am working on a project, and I periodically save versions of it, those versions, which are different files, may have identical files or folders within them. You cannot remove duplicates within them without breaking the entire saved version. So, I may have project files 1, 2, and 3, and #2 and #3 have the same files in the their internal "Media" folders but are different versions of the file and need to retain their internal structure including the Media folders, whereas #1 and #2 are literal duplicates of the same exact Logic Pro saved file. Dupeguru has no way of telling me "1 and 2 are duplicates, 2 and 3 are not".

In fact, it gets worse, because sometimes to top level of project files consist ONLY of nested folders, with all content in the subfolders. So there is literally no way to know if two Logic projects are identical, because you can't see in Dupeguru when ALL the subfolder contents are duplicate for a given Logic file and therefore the files are duplicates, or one some are identical but others are different and therefore the files are not duplicates. So, you can't tell it to remove the Media, Alternatives, and Resources subfolders from the dupe results... for some files, those subfolders are all there are in the file, if you don't look at them you're not looking at that file at all.

EDIT: It does the same thing with .rtfd files. If you have two different RTF docs saved as .rtfd, which happen to share an image file between them, it reports the image files as duplicates even though two different documents depend on them and may break if you remove the "duplicate" file.

Describe the solution you'd like
I want Dupeguru to recognize Logic Pro (and similar, such as .rtfd) saved package "files" as if they are normal files: report them as duplicates if they are duplicates. But not report on duplicate subfolders or files within the file packages as duplicates if the overall file packages containing them are not duplicates and individually require the "duplicate" subfolders or files not to be removed.

Even though these are folders on disk, MacOS treats them as single files for all user-facing purposes, not as folders. I'd like Dupeguru to obey the OS's UX standard on that. Dupeguru is the only thing I use anywhere in the MacOS platform where these turn, from a user perspective, from files into folders.

Describe alternatives you've considered
I have tried setting the scan type to folders but I'm not clear what this does, it definitely doesn't say "1 and 2 are duplicates, 2 and 3 are not", it just turns up all the internal duplicate folders that shouldn't be touched. I do see that duplicate Logic Pro file packages are not turning up as duplicates using this method.

I do know duplicates can be replaced with hard links, but the 99% of the time I'm dealing with non-Logic files I don't want to do this, so either way this requires manually going through my Logic Pro files and handling them totally separately from all other files.

I could individually compress each of my Logic Pro saved files into zip archives before running Dupeguru and uncompressing after them, but for dozens of files or more, this becomes a pain.

At this point I am only able to go through and compare my Logic Pro files looking for duplicates (of which I have many, due to a recent Dropbox snafu as mentioned in an another issue) by hand, it doesn't seem doable with Dupeguru.

(Later edit: everything in this section applies to .rtfd files also.)