I'm gonna Won't Fix this; while the logical flow between pipetask subcommands (and by extension, BPS) can certainly be hard to follow, I think the real fix is a reworking of those subcommands and the boundaries between them, because even a nice flowchart would be hard to follow now (and I hate spending time writing documentation as a workaround for interface problems). If we do that well, I think a few examples will then do the job even better than a flowchart, but we'll see. In any case, keeping a ticket with a Gen2-specific description around as a placeholder for "fix the pipetask/BPS docs" doesn't seem useful. New tickets are cheap.
Where does this ticket stand in the gen3 world with runQuantum?