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If they use an open standard interface like Jtag, then it would be possible. We tried with AVR, but the Jtag interface is not totally open.
It's hard to do that. We need to work on both sides at the same time. For example, we are now trying to figure out the data transfer protocol, and we need to program both Window and Linux.
The gdb protocol for reading is:
$ m , # $ m , # with + (ACK) and - (NAK)
We would need protocol extensions to write to buffer, then a write flash command.
But they all use web servers, and many of them are Linux. As long as they don't have to touch them, it would be fine. Think of it as a Jtag programming server.
We don't want the client to mess with the Linux box as all. All the user interfaces will be done on the Window side. The Linux box will be running on read-only 64M Flash Drive. There is no user interface to it, except for an RJ-45 for network and a USB cable for programming the target.
No problem, you will need a uC eventually, for another project.