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flash updating

I'm trying to implement a way to update file (remotely) that resides on my file system which is currently up and running. It seems that the best way to do this is to update the entire compressed filesystem in flash through some user level app.
Since the bootloader does not exist as far as the kernel is concern (once the kernel is decompressed), I figure their's only two other alternatives: reboot and enter some update mode, or a user app.

My questions are, Do I need to give the app some special permission to be able to write to flash? Or is this a good approach at all? Is their an already existing method to do this sort of thing?

Any thoughts on the subject will be appreciated. I'm on an ARM9 platform with 2.6 kernel.

Much thanks,

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