Hi,
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My point about readra/readrb is that the logic that handles the pipeline stall doesn't really want to look that far into the instruction decode.
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Maybe, Altera uses embedded memories for the Nios's register files, and sets those in the same clock phase of the 'Decode Stage'. To read the contents of the embedded memories, it takes one clock, so the RA & RB field data must be sent directly from the 'Fetch Stage' to the register file. The contents of the register file are always discharged to the following stage even when those are not used. But to avoid the 'RAW' hazard, the 'Decode Stage' must decide whether the RA and RB are really used or not. I don't know whether Altera uses readra and readrb bits for this purpose or not, because the 'R0' register can be used instead of those.
Kazu