If you want to get fancy, I saw someone testing OGG files

which does have the ability to package multitracks into one file, but not many daws support creating these, but might get fancy and package them up for storage that way…

But realistically just have a dominate audio file and a way to upload a folder of other files attached to the same note

As far as the tree of referencing is concerned… I think you just have a field to mention the notes you found the samples you used, like a quote note.