deprecate init/repo-init command

In current workflow you need to run setup to run init (because of
repository name), but you need to run init before setup (because of
repository tree rights).

New solution just add `Repo.init()` method call to setup subcommand
after config reload to make sure that repository name has been applied.
In addition chown method as well as setuid method for check_output have
been added.

tests/testresources/core/ahriman.ini

@@ -25,7 +25,7 @@ makepkg_flags = --skippgpcheck
 
 [repository]
 name = aur-clone
-root = /var/lib/ahriman
+root = ../../../
 
 [sign]
 target =