core: Associate branches with remotes, move trigger runs into checkout

Also add --atomic-retarget option to checkout. This does the magical
symlink dance to do atomic swaps between trees.

tests/t0000-basic.sh

@@ -19,7 +19,7 @@
 
 set -e
 
-echo "1..28"
+echo "1..30"
 
 . libtest.sh
 
@@ -206,3 +206,16 @@ cmp union-files-count{,.new}
 cd checkout-test2-union
 assert_file_has_content ./yet/another/tree/green "leaf"
 echo "ok checkout union 1"
+
+cd ${test_tmpdir}
+$OSTREE checkout --atomic-retarget test2 checkout-atomic-test2
+cd checkout-atomic-test2
+assert_file_has_content ./yet/another/tree/green "leaf"
+echo "ok checkout atomic"
+
+cd ${test_tmpdir}
+rm -rf test2
+$OSTREE checkout --atomic-retarget test2
+cd test2
+assert_file_has_content ./yet/another/tree/green "leaf"
+echo "ok checkout short form"