This problem has been around for decades. When I was at Microsoft in the late 80s and early 90s, I helped write OLE (object linking and embedding). This included work on Microsoft’s compound documents, which basically turned a document file into a directory, and Apple’s packages seem to be the same. I never understood why writing this code was necessary, given that zip files already had this functionality.
Later, I worked on Scientific WorkPlace. Our file extension was .sci, but it was really a zip file, since it used TeX, and TeX has the same problem of having documents dependent on graphics which can get separated from the main document. Another problem with TeX is that when you try to delete outdated graphics file, you have no idea which ones are still needed by some TeX document.
Using Zip files solved those problems. Given that DevonThink is Mac-only, I would suggest looking at using Apple’s packages. If TextBundles are what I have seen Brett Terpstra discussing. then I would guess that they are also very close to zip files.
The .sci files in Scientific WorkPlace were zip files with no compression. If you opened one in a text editor, it was readable as text.