In my opinion, the Web Applications Packaging Format Requirements document is too much concerned with WAPF documents being files, rather than resources. It mentions even such things as recommended (SHOULD?) extensions, their treatment by operating systems when they don't know the MIME type and by servers, directories (presumably a tree) and length of file names. (If such considerations were in scope of WAPF spec, they'd be as well for HTML, CSS, XBL etc.!)
Why not simply reuse existing MIME capabilities and mint a new multipart subtype? This would at hand provide solutions for encoding, linking (cid:), optional compression (gzip support could be required), external bodies, hooks for any accompanying metadata per component (MIME headers) and many other features.
