IIUC, based on skimming some of the code, this seems to be for people who want to layout their home directory according to the conventions that the XDG group suggested [1], well into the history of Unix-y systems.
For example, a given tool, `foo`, might've originally created a `~/.foo/` directory, which `foo` still supports for backward compatibility, but `foo` now prefers XDG convention `~/.config/foo/`. `xdg-ninja` can inform you of that, and help you move the directory.
For another example, tool `bar` might still default to config file `~/.barrc`, but `xdg-ninja` might advise you to move it to XDG-like `~/.config/bar/rc`, and to set `bar`'s `BARRC` environment variable to point to that, even though `bar` doesn't use XDG conventions directly.
[1] https://specifications.freedesktop.org/basedir-spec/latest/