I suppose this has recently changed in #1706. The current prompt is confusing to me:

$ gh pr create
? Which should be the base repository (used for e.g. querying issues) for this directory?  [Use arrows to move, type to filter]
> liberapay/liberapay.com
  waldyrious/liberapay.com

There are two issues here:

1. I am not sure what "base repository" means here; my mental model when creating a PR is one of "source" (e.g. my fork) and "target" (e.g. upstream), and I could interpret "base" as referring to either of these.
2. It's not clear what "for this directory" means. I would expect something like "...for this PR", but I guess something different is being asked here, and the message doesn't tell me what.