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That’s a really good question, and you’ve got the current behavior right.
At the moment, the Altair-Duino 680 emulates a single MC6850 ACIA at $F000/$F001. The serial-port selection at startup determines which physical Arduino port is connected to that emulated ACIA. So the USB programming port and the RS-232/UART connection are currently alternative console connections - they are not exposed to the 6800 as two independent serial devices.
That means $F007 is currently unmapped, so software expecting a second serial interface there, such as the FLEX serial disk driver in the Mike Douglas setup, won’t have anything to talk to.
The good news is that this should be quite feasible to add. The Due has multiple hardware UARTs, so I could emulate a second serial interface at the addresses expected by the UIO board and route that to one of the unused Arduino serial ports. In that configuration you could have, for example:
That would be much better than simply providing another selectable console port, because software running on the emulated 680 would actually see two separate serial devices, just as it would with the appropriate expansion hardware on a real machine.
I haven’t implemented that second interface yet, but this FLEX disk-server use case is a very good reason to do it. I’d like to research the original UIO register/address behavior first so that I emulate the board rather than just special-case $F007. It may take me some time but it's a clear goal.
And thanks - I’m glad you’re enjoying the kit!