I’m generally appalled at the state of compound documents…
In the Apple world, Mac apps like Keynote love to use bundled directories which look like flat files at the UI level. Cute, but Thunderbird gleefully destroys them as attachments… Apple’s Mail.app transparently packages them into .zip archives for you, but Thunderbird just gives you a file with a directory listing, which naturally enough fails to open when you download it. Nice!
OpenOffice and the latest greatest MS Office stick their XML documents into a .zip archive and package image files, etc into that archive. These actually do act like flat files, so attachments and uploads work. :) But it makes file type detection and validation a little harder; verifying which file type your zip thingy is and whether it contains extra files slipped in…
And then you get fun packages like Scribus, which just give you an XML file referencing all your external image files by path, leaving no way to transfer your entire document without manually managing a directory structure and sending around or archiving multiple files manually.
We had a request for allowing Scribus uploads to Wikimedia sites for things like PR materials… sounds great, except for how any actually relevant document will need image files packed into the same directory which you can’t do. D’oh!