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

Documentation/technical/commit-graph.txt

@@ -112,12 +112,24 @@ Design Details
 - The file format includes parameters for the object ID hash function,
   so a future change of hash algorithm does not require a change in format.
 
+- Commit grafts and replace objects can change the shape of the commit
+  history. The latter can also be enabled/disabled on the fly using
+  `--no-replace-objects`. This leads to difficultly storing both possible
+  interpretations of a commit id, especially when computing generation
+  numbers. The commit-graph will not be read or written when
+  replace-objects or grafts are present.
+
+- Shallow clones create grafts of commits by dropping their parents. This
+  leads the commit-graph to think those commits have generation number 1.
+  If and when those commits are made unshallow, those generation numbers
+  become invalid. Since shallow clones are intended to restrict the commit
+  history to a very small set of commits, the commit-graph feature is less
+  helpful for these clones, anyway. The commit-graph will not be read or
+  written when shallow commits are present.
+
 Future Work
 -----------
 
-- The commit graph feature currently does not honor commit grafts. This can
-  be remedied by duplicating or refactoring the current graft logic.
-
 - After computing and storing generation numbers, we must make graph
   walks aware of generation numbers to gain the performance benefits they
   enable. This will mostly be accomplished by swapping a commit-date-ordered