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.

src/libostree/ostree.h

@@ -27,5 +27,6 @@
 #include <ostree-mutable-tree.h>
 #include <ostree-repo-file.h>
 #include <ostree-traverse.h>
+#include <ostree-sysroot.h>
 
 #endif