t4129: fix racy index when calling chmod after git-add

This patch fixes a racy test failure in t4129.

The deletion test added by e95d515 (apply: canonicalize modes read
from patches, 2024-08-05) wants to make sure that git-apply does not
complain about a non-canonical mode in the patch, even if that mode does
not match the working tree file. So it does this:

	echo content >non-canon &&
	git add non-canon &&
	chmod 666 non-canon &&

This is wrong, because running chmod will update the ctime on the file,
making it stat-dirty and causing git-apply to refuse to apply the patch.
But this only happens sometimes, since it depends on the timestamps
crossing a second boundary (but it triggers pretty quickly when run with
--stress).

We can fix this by doing the chmod before updating the index. The order
isn't important here, as the mode will be canonicalized to 100644 in the
index anyway (in fact, the chmod is not even that important in the first
place, since git-apply will only look at the index; I only added it as
an extra confirmation that git-apply would not be confused by it).

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

Author: peff

t/t4129-apply-samemode.sh

@@ -153,8 +153,8 @@ test_expect_success POSIXPERM 'patch mode for new file is canonicalized' '
 test_expect_success POSIXPERM 'patch mode for deleted file is canonicalized' '
 	test_when_finished "git reset --hard" &&
 	echo content >non-canon &&
-	git add non-canon &&
 	chmod 666 non-canon &&
+	git add non-canon &&
 
 	cat >patch <<-\EOF &&
 	diff --git a/non-canon b/non-canon