Emacs

Some emacs modes rely on project.el to discover workspace roots. project.el's heuristics include checks for .git, which will fail in jj repositories that are not colocated. This can be addressed by adding ".jj" to project-vc-extra-root-markers, e.g.:

(use-package project
  :config
  (add-to-list 'project-vc-extra-root-markers ".jj"))