I agree. I hate monkeying (too much ]:D) with the Arduino directory. It's also nice that libraries and third-party cores now survive an upgrade.
If I may suggest, that particular light has been hidden under a bushel a bit. I never spotted that process documented anywhere (no doubt it is, but no-one pointed me to it).
I honestly cannot remember where (or even if) I read about the new directory structure. The only reason I know it so well is from maintaining the Tiny Core.