Fair enough, and it appears you are right, now that I found this issue on one of the HomeBrew repositories: Homebrew/homebrew-cask#58046 (posted by a HomeBrew crew member).
Although this appears to be a HomeBrew issue, maybe it's a good idea to leave this issue open for awhile so other Geany users, updating though HomeBrew will be aware of this. It appears that all apps with pre-mavericks references suffer here (but as Geany is the only app (which got a new version since this bug came in) I had, I wasn't sure if where the blame was). 😉