Create destroy_commit_graph() method to delete the commit-graph file
when history is altered by a replace-object call. If the commit-graph
is rebuilt after that, we will load the correct object while reading
the commit-graph.

When parsing a commit, first check if the commit was grafted. If so,
then ignore the commit-graph for that commit and insted use the parents
loaded by parsing the commit buffer and comparing against the graft
file. 

Signed-off-by: Derrick Stolee <dsto...@microsoft.com>
---
 builtin/replace.c |  3 +++
 commit-graph.c    | 20 +++++++++++++++++++-
 commit-graph.h    |  9 +++++++++
 commit.c          |  5 +++++
 4 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/builtin/replace.c b/builtin/replace.c
index 9f01f3fc7f..d553aadcdc 100644
--- a/builtin/replace.c
+++ b/builtin/replace.c
@@ -15,6 +15,7 @@
 #include "parse-options.h"
 #include "run-command.h"
 #include "tag.h"
+#include "commit-graph.h"
 
 static const char * const git_replace_usage[] = {
        N_("git replace [-f] <object> <replacement>"),
@@ -468,6 +469,8 @@ int cmd_replace(int argc, const char **argv, const char 
*prefix)
                usage_msg_opt("--raw only makes sense with --edit",
                              git_replace_usage, options);
 
+       destroy_commit_graph(get_object_directory());
+
        switch (cmdmode) {
        case MODE_DELETE:
                if (argc < 1)
diff --git a/commit-graph.c b/commit-graph.c
index e9195dfb17..95af4ed519 100644
--- a/commit-graph.c
+++ b/commit-graph.c
@@ -6,6 +6,7 @@
 #include "pack.h"
 #include "packfile.h"
 #include "commit.h"
+#include "dir.h"
 #include "object.h"
 #include "refs.h"
 #include "revision.h"
@@ -240,15 +241,22 @@ static struct commit_list **insert_parent_or_die(struct 
commit_graph *g,
 {
        struct commit *c;
        struct object_id oid;
+       const unsigned char *real;
 
        if (pos >= g->num_commits)
                die("invalid parent position %"PRIu64, pos);
 
        hashcpy(oid.hash, g->chunk_oid_lookup + g->hash_len * pos);
+
+       real = lookup_replace_object(oid.hash);
+
        c = lookup_commit(&oid);
        if (!c)
                die("could not find commit %s", oid_to_hex(&oid));
-       c->graph_pos = pos;
+
+       if (!hashcmp(real, oid.hash))
+               c->graph_pos = pos;
+
        return &commit_list_insert(c, pptr)->next;
 }
 
@@ -1019,3 +1027,13 @@ int verify_commit_graph(struct commit_graph *g)
 
        return verify_commit_graph_error;
 }
+
+void destroy_commit_graph(const char *obj_dir)
+{
+       char *graph_name;
+       close_commit_graph();
+
+       graph_name = get_commit_graph_filename(obj_dir);
+       remove_path(graph_name);
+       FREE_AND_NULL(graph_name);
+}
diff --git a/commit-graph.h b/commit-graph.h
index 9a06a5f188..1d17da1582 100644
--- a/commit-graph.h
+++ b/commit-graph.h
@@ -56,4 +56,13 @@ void write_commit_graph(const char *obj_dir,
 
 int verify_commit_graph(struct commit_graph *g);
 
+/*
+ * Delete the commit-graph file in the given object directory.
+ *
+ * WARNING: this deletes data, so should only be used when
+ * performing history-altering actions like replace-object
+ * or grafts.
+ */
+void destroy_commit_graph(const char *obj_dir);
+
 #endif
diff --git a/commit.c b/commit.c
index 6eaed0174c..2fe31cde77 100644
--- a/commit.c
+++ b/commit.c
@@ -403,6 +403,11 @@ int parse_commit_internal(struct commit *item, int 
quiet_on_missing, int use_com
                return -1;
        if (item->object.parsed)
                return 0;
+
+       prepare_commit_graft();
+       if (commit_graft_pos(item->object.oid.hash) >= 0)
+               use_commit_graph = 0;
+
        if (use_commit_graph && parse_commit_in_graph(item))
                return 0;
        buffer = read_sha1_file(item->object.oid.hash, &type, &size);
-- 
2.16.2.338.gcfe06ae955

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