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There's a VMU filesystem support patch released for the Linux kernel:
Adrian McNenamin wrote:The only physical VMUs released were limited to 128K of memory but it
was generally believed that Sega planned to introduce devices with
bigger memories and certainly the syntax of the filesystem, which I
call VMUFAT, allows for larger volumes.
Some years ago I contributed a driver for the VMU's flash and
attempted to contribute one for the filesystem (see https://lkml.org/lkml/2009/2/14/127 for instance).
While it might be too soon to know if it'll be merged into the mainline kernel, the patch can be found on the Linux Kernel Mailing List.
The only practical application I could think of for this is making DC emulators for Linux use a separate partition for saves, but that doesn't make much sense.
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You can mount files as filesystems. So you could essentially have an image of a memory card and mount it as a file.
That said, I don't really see how it would help Dreamcast emulators, since it'd be more difficult to intercept the calls to write files to a memory card than to just do things at a low-level anyway.