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

commit-graph.h

@@ -69,6 +69,7 @@ void write_commit_graph(const char *obj_dir,
 
 int verify_commit_graph(struct repository *r, struct commit_graph *g);
 
+void close_commit_graph(struct repository *);
 void free_commit_graph(struct commit_graph *);
 
 #endif