Uma opção é usar unionfs
Unionfs: A Stackable Unification File System
This project builds a stackable unification file system, which can appear to merge the contents of several directories (branches), while keeping their physical content separate. Unionfs is useful for unified source tree management, merged contents of split CD-ROM, merged separate software package directories, data grids, and more. Unionfs allows any mix of read-only and read-write branches, as well as insertion and deletion of branches anywhere in the fan-out.
Ou outra opção semelhante aufs .