Now this is a hack: Chris Dolan has written Fuse::PDF, a Perl module to embedd a filesystem (including meta-data) inside a PDF-file. From the documentation:
The Adobe Portable Document Format is an arbitrary collection of nodes which support a tree structure. Most of that data is oriented toward document rendering, but it’s legal to add arbitrarily complex data virtually anywhere in the document structure.
By deciding on a convention for representing a filesystem data and leveraging the FUSE (Filesystem in Userspace) library, we map filesystem calls to PDF edits.