Is it possible to run with a ramdisk, and then every 20-30 minutes or so
copy the relevant files from the ramdisk to the flash disk?  If the set
of files the user can change is fixed, you can do this with a simple
script.  If the file system is small, your copy program could traverse
the ramdisk tree, and copy only those files whose modtimes have changed,
or which have been created since the last copy.  Since it is traversing
a ramdisk structure it would be reasonably fast.

This doesn't really solve your problem very well, since you might lose
20-30 minutes of data.  Also, if you don't have a lot of cycles to
spare, the copy process may cause you to miss some deadlines, unless
the copy is quick.

If the copy is quick, perhaps you could capture the I/O system calls,
by interposing a shared library, and then keep a list of altered files
in some sort of shared memory area.  This seems like a hack, doesn't it.

Does this make sense?

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