commit-graph: prepare commit graph

Before checking if the repository has a commit-graph loaded, be sure
to run prepare_commit_graph(). This is necessary because otherwise
the topo_levels slab is not initialized. As we compute topo_levels for
the new commits, we iterate further into the lower layers since the
first visit to each commit looks as though the topo_level is not
populated.

By properly initializing the topo_slab, we fix the previously broken
case of a split commit graph where a base layer has the
generation_data_overflow chunk.

Signed-off-by: Derrick Stolee <dstolee@microsoft.com>

commit-graph.c

@@ -2348,6 +2348,7 @@ int write_commit_graph(struct object_directory *odb,
 	init_topo_level_slab(&topo_levels);
 	ctx->topo_levels = &topo_levels;
 
+	prepare_commit_graph(ctx->r);
 	if (ctx->r->objects->commit_graph) {
 		struct commit_graph *g = ctx->r->objects->commit_graph;
 
@@ -2361,7 +2362,6 @@ int write_commit_graph(struct object_directory *odb,
 		ctx->changed_paths = 1;
 	if (!(flags & COMMIT_GRAPH_NO_WRITE_BLOOM_FILTERS)) {
 		struct commit_graph *g;
-		prepare_commit_graph_one(ctx->r, ctx->odb);
 
 		g = ctx->r->objects->commit_graph;
 
@@ -2373,10 +2373,7 @@ int write_commit_graph(struct object_directory *odb,
 	}
 
 	if (ctx->split) {
-		struct commit_graph *g;
-		prepare_commit_graph(ctx->r);
-
-		g = ctx->r->objects->commit_graph;
+		struct commit_graph *g = ctx->r->objects->commit_graph;
 
 		while (g) {
 			ctx->num_commit_graphs_before++;
@@ -2400,9 +2397,6 @@ int write_commit_graph(struct object_directory *odb,
 
 	ctx->approx_nr_objects = approximate_object_count();
 
-	if (ctx->append)
-		prepare_commit_graph_one(ctx->r, ctx->odb);
-
 	if (ctx->append && ctx->r->objects->commit_graph) {
 		struct commit_graph *g = ctx->r->objects->commit_graph;
 		for (i = 0; i < g->num_commits; i++) {

t/t5318-commit-graph.sh

@@ -446,7 +446,7 @@ test_expect_success 'warn on improper hash version' '
 	)
 '
 
-test_expect_failure 'lower layers have overflow chunk' '
+test_expect_success 'lower layers have overflow chunk' '
 	cd "$TRASH_DIRECTORY/full" &&
 	UNIX_EPOCH_ZERO="@0 +0000" &&
 	FUTURE_DATE="@2147483646 +0000" &&