I agree with @mcd. Using links and displays, as suggested by @hkfto works, but can cause problems and shouldn't be used across an entire story, since both Harlowe and SugarCube rely on passage transitions for important engine functions.
I haven't really used paloma extensively, but it seems like a great format. I would probably recommend it over Jonah; Jonah is old and no longer maintained, and you'll likely have issues using it. For example, it won't work in newer versions of Safari, and I wouldn't be surprised if it's days are numbered on other browsers as well.