Merge branch 'ds/commit-graph-with-grafts'

The recently introduced commit-graph auxiliary data is incompatible
with mechanisms such as replace & grafts that "breaks" immutable
nature of the object reference relationship.  Disable optimizations
based on its use (and updating existing commit-graph) when these
incompatible features are in use in the repository.

* ds/commit-graph-with-grafts:
  commit-graph: close_commit_graph before shallow walk
  commit-graph: not compatible with uninitialized repo
  commit-graph: not compatible with grafts
  commit-graph: not compatible with replace objects
  test-repository: properly init repo
  commit-graph: update design document
  refs.c: upgrade for_each_replace_ref to be a each_repo_ref_fn callback
  refs.c: migrate internal ref iteration to pass thru repository argument

upload-pack.c

@@ -24,6 +24,7 @@
 #include "quote.h"
 #include "upload-pack.h"
 #include "serve.h"
+#include "commit-graph.h"
 #include "commit-reach.h"
 
 /* Remember to update object flag allocation in object.h */
@@ -692,6 +693,7 @@ static void deepen_by_rev_list(int ac, const char **av,
 {
 	struct commit_list *result;
 
+	close_commit_graph(the_repository);
 	result = get_shallow_commits_by_rev_list(ac, av, SHALLOW, NOT_SHALLOW);
 	send_shallow(result);
 	free_commit_list(result);