Speed up file upload enormously.

We need to start with a long serial timeout, in order to catch the reboot
messages for a firmware upload (this has to be done through the bootloader).
But once we start sending the file, cut the serial timeout to 1ms. (I've
tested it down to 1us, but that may not work for everyone, and it doesn't
improve performance in a statistically significant way.)

This brings the time to upload a 4.5MB bitstream from 38:23 to 1:25.

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