commit-graph: disable GIT_COMMIT_GRAPH_PARANOIA by default

In 7a5d604 (commit: detect commits that exist in commit-graph but not
in the ODB, 2023-10-31), we have introduced a new object existence check
into `repo_parse_commit_internal()` so that we do not parse commits via
the commit-graph that don't have a corresponding object in the object
database. This new check of course comes with a performance penalty,
which the commit put at around 30% for `git rev-list --topo-order`. But
there are in fact scenarios where the performance regression is even
higher. The following benchmark against linux.git with a fully-build
commit-graph:

  Benchmark 1: git.v2.42.1 rev-list --count HEAD
    Time (mean ± σ):     658.0 ms ±   5.2 ms    [User: 613.5 ms, System: 44.4 ms]
    Range (min … max):   650.2 ms … 666.0 ms    10 runs

  Benchmark 2: git.v2.43.0-rc1 rev-list --count HEAD
    Time (mean ± σ):      1.333 s ±  0.019 s    [User: 1.263 s, System: 0.069 s]
    Range (min … max):    1.302 s …  1.361 s    10 runs

  Summary
    git.v2.42.1 rev-list --count HEAD ran
      2.03 ± 0.03 times faster than git.v2.43.0-rc1 rev-list --count HEAD

While it's a noble goal to ensure that results are the same regardless
of whether or not we have a potentially stale commit-graph, taking twice
as much time is a tough sell. Furthermore, we can generally assume that
the commit-graph will be updated by git-gc(1) or git-maintenance(1) as
required so that the case where the commit-graph is stale should not at
all be common.

With that in mind, default-disable GIT_COMMIT_GRAPH_PARANOIA and restore
the behaviour and thus performance previous to the mentioned commit. In
order to not be inconsistent, also disable this behaviour by default in
`lookup_commit_in_graph()`, where the object existence check has been
introduced right at its inception via f559d6d (revision: avoid
hitting packfiles when commits are in commit-graph, 2021-08-09).

This results in another speedup in commands that end up calling this
function, even though it's less pronounced compared to the above
benchmark. The following has been executed in linux.git with ~1.2
million references:

  Benchmark 1: GIT_COMMIT_GRAPH_PARANOIA=true git rev-list --all --no-walk=unsorted
    Time (mean ± σ):      2.947 s ±  0.003 s    [User: 2.412 s, System: 0.534 s]
    Range (min … max):    2.943 s …  2.949 s    3 runs

  Benchmark 2: GIT_COMMIT_GRAPH_PARANOIA=false git rev-list --all --no-walk=unsorted
    Time (mean ± σ):      2.724 s ±  0.030 s    [User: 2.207 s, System: 0.514 s]
    Range (min … max):    2.704 s …  2.759 s    3 runs

  Summary
    GIT_COMMIT_GRAPH_PARANOIA=false git rev-list --all --no-walk=unsorted ran
      1.08 ± 0.01 times faster than GIT_COMMIT_GRAPH_PARANOIA=true git rev-list --all --no-walk=unsorted

So whereas 7a5d604 initially introduced the logic to start doing an
object existence check in `repo_parse_commit_internal()` by default, the
updated logic will now instead cause `lookup_commit_in_graph()` to stop
doing the check by default. This behaviour continues to be tweakable by
the user via the GIT_COMMIT_GRAPH_PARANOIA environment variable.

Note that this requires us to amend some tests to manually turn on the
paranoid checks again. This is because we cause repository corruption by
manually deleting objects which are part of the commit graph already.
These circumstances shouldn't usually happen in repositories.

Reported-by: Jeff King <[email protected]>
Signed-off-by: Patrick Steinhardt <[email protected]>
Signed-off-by: Junio C Hamano <[email protected]>

Author: pks-t

Documentation/git.txt

@@ -917,9 +917,9 @@ for full details.
 	avoid issues with stale commit-graphs that contain references to
 	already-deleted commits, but comes with a performance penalty.
 +
-The default is "true", which enables the aforementioned behavior.
-Setting this to "false" disables the existence check. This can lead to
-a performance improvement at the cost of consistency.
+The default is "false", which disables the aforementioned behavior.
+Setting this to "true" enables the existence check so that stale commits
+will never be returned from the commit-graph at the cost of performance.
 
 `GIT_ALLOW_PROTOCOL`::
 	If set to a colon-separated list of protocols, behave as if

commit-graph.c

@@ -1029,7 +1029,7 @@ struct commit *lookup_commit_in_graph(struct repository *repo, const struct obje
 	uint32_t pos;
 
 	if (commit_graph_paranoia == -1)
-		commit_graph_paranoia = git_env_bool(GIT_COMMIT_GRAPH_PARANOIA, 1);
+		commit_graph_paranoia = git_env_bool(GIT_COMMIT_GRAPH_PARANOIA, 0);
 
 	if (!prepare_commit_graph(repo))
 		return NULL;

commit.c

@@ -577,7 +577,7 @@ int repo_parse_commit_internal(struct repository *r,
 		static int commit_graph_paranoia = -1;
 
 		if (commit_graph_paranoia == -1)
-			commit_graph_paranoia = git_env_bool(GIT_COMMIT_GRAPH_PARANOIA, 1);
+			commit_graph_paranoia = git_env_bool(GIT_COMMIT_GRAPH_PARANOIA, 0);
 
 		if (commit_graph_paranoia && !has_object(r, &item->object.oid, 0)) {
 			unparse_commit(r, &item->object.oid);

t/t5318-commit-graph.sh

@@ -909,10 +909,10 @@ test_expect_success 'stale commit cannot be parsed when given directly' '
 
 		# Verify that it is possible to read the commit from the
 		# commit graph when not being paranoid, ...
-		GIT_COMMIT_GRAPH_PARANOIA=false git rev-list B &&
+		git rev-list B &&
 		# ... but parsing the commit when double checking that
 		# it actually exists in the object database should fail.
-		test_must_fail git rev-list -1 B
+		test_must_fail env GIT_COMMIT_GRAPH_PARANOIA=true git rev-list -1 B
 	)
 '
 
@@ -936,9 +936,9 @@ test_expect_success 'stale commit cannot be parsed when traversing graph' '
 
 		# Again, we should be able to parse the commit when not
 		# being paranoid about commit graph staleness...
-		GIT_COMMIT_GRAPH_PARANOIA=false git rev-parse HEAD~2 &&
+		git rev-parse HEAD~2 &&
 		# ... but fail when we are paranoid.
-		test_must_fail git rev-parse HEAD~2 2>error &&
+		test_must_fail env GIT_COMMIT_GRAPH_PARANOIA=true git rev-parse HEAD~2 2>error &&
 		grep "error: commit $oid exists in commit-graph but not in the object database" error
 	)
 '

t/t6022-rev-list-missing.sh

@@ -13,6 +13,12 @@ test_expect_success 'create repository and alternate directory' '
 	test_commit 3
 '
 
+# We manually corrupt the repository, which means that the commit-graph may
+# contain references to already-deleted objects. We thus need to enable
+# commit-graph paranoia to not returned these deleted commits from the graph.
+GIT_COMMIT_GRAPH_PARANOIA=true
+export GIT_COMMIT_GRAPH_PARANOIA
+
 for obj in "HEAD~1" "HEAD~1^{tree}" "HEAD:1.t"
 do
 	test_expect_success "rev-list --missing=error fails with missing object $obj" '

t/t7700-repack.sh

@@ -271,7 +271,7 @@ test_expect_success 'repacking fails when missing .pack actually means missing o
 		ls .git/objects/pack/*.pack >before-pack-dir &&
 
 		test_must_fail git fsck &&
-		test_must_fail git repack --cruft -d 2>err &&
+		test_must_fail env GIT_COMMIT_GRAPH_PARANOIA=true git repack --cruft -d 2>err &&
 		grep "bad object" err &&
 
 		# Before failing, the repack did not modify the