diff --git a/Documentation/RelNotes/2.41.0.txt b/Documentation/RelNotes/2.41.0.txt
index af9f3fd73084c8..8a9e17016e45ee 100644
--- a/Documentation/RelNotes/2.41.0.txt
+++ b/Documentation/RelNotes/2.41.0.txt
@@ -65,9 +65,9 @@ UI, Workflows & Features
    has symbolic links inside its $GIT_DIR; an error message when that
    happens has been updated.
 
- * "git branch --format=..." and "git format-patch --format=..."
-   learns "--omit-empty" to hide refs that whose formatting result
-   becomes an empty string from the output.
+ * The "--format=..." option of "git for-each-ref", "git branch", and
+   "git tag" commands learn "--omit-empty" to hide refs whose
+   formatting results in an empty string from the output.
 
  * The sendemail-validate validate hook learned to pass the total
    number of input files and where in the sequence each invocation is
@@ -369,6 +369,10 @@ Fixes since v2.40
     by git forges to disable replace-refs feature.
    (merge b6551feadf ds/merge-tree-use-config later to maint).
 
+ * A few bugs in the sequencer machinery that results in miscounting
+   the steps have been corrected.
+   (merge 170eea9750 js/rebase-count-fixes later to maint).
+
  * Other code cleanup, docfix, build fix, etc.
    (merge f7111175df as/doc-markup-fix later to maint).
    (merge 90ff7c9898 fc/test-aggregation-clean-up later to maint).
diff --git a/Documentation/config/http.txt b/Documentation/config/http.txt
index c9aa1428556ed2..10b118227e3bc9 100644
--- a/Documentation/config/http.txt
+++ b/Documentation/config/http.txt
@@ -253,8 +253,9 @@ significantly since the entire buffer is allocated even for small
 pushes.
 
 http.lowSpeedLimit, http.lowSpeedTime::
-	If the HTTP transfer speed is less than 'http.lowSpeedLimit'
-	for longer than 'http.lowSpeedTime' seconds, the transfer is aborted.
+	If the HTTP transfer speed, in bytes per second, is less than
+	'http.lowSpeedLimit' for longer than 'http.lowSpeedTime' seconds,
+	the transfer is aborted.
 	Can be overridden by the `GIT_HTTP_LOW_SPEED_LIMIT` and
 	`GIT_HTTP_LOW_SPEED_TIME` environment variables.
 
diff --git a/GIT-VERSION-GEN b/GIT-VERSION-GEN
index 9a1111af9b14f3..2ef084f02ad806 100755
--- a/GIT-VERSION-GEN
+++ b/GIT-VERSION-GEN
@@ -1,7 +1,7 @@
 #!/bin/sh
 
 GVF=GIT-VERSION-FILE
-DEF_VER=v2.40.GIT
+DEF_VER=v2.41.0-rc2
 
 LF='
 '
diff --git a/sequencer.c b/sequencer.c
index b553b49fbb64e7..bceb6abcb6c733 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -2477,7 +2477,6 @@ void todo_list_release(struct todo_list *todo_list)
 static struct todo_item *append_new_todo(struct todo_list *todo_list)
 {
 	ALLOC_GROW(todo_list->items, todo_list->nr + 1, todo_list->alloc);
-	todo_list->total_nr++;
 	return todo_list->items + todo_list->nr++;
 }
 
@@ -2668,7 +2667,7 @@ int todo_list_parse_insn_buffer(struct repository *r, char *buf,
 	char *p = buf, *next_p;
 	int i, res = 0, fixup_okay = file_exists(rebase_path_done());
 
-	todo_list->current = todo_list->nr = 0;
+	todo_list->current = todo_list->nr = todo_list->total_nr = 0;
 
 	for (i = 1; *p; i++, p = next_p) {
 		char *eol = strchrnul(p, '\n');
@@ -2689,6 +2688,9 @@ int todo_list_parse_insn_buffer(struct repository *r, char *buf,
 			item->commit = NULL;
 		}
 
+		if (item->command != TODO_COMMENT)
+			todo_list->total_nr++;
+
 		if (fixup_okay)
 			; /* do nothing */
 		else if (is_fixup(item->command))
@@ -4270,7 +4272,7 @@ void todo_list_filter_update_refs(struct repository *r,
 		if (!is_null_oid(&rec->after))
 			continue;
 
-		for (j = 0; !found && j < todo_list->total_nr; j++) {
+		for (j = 0; !found && j < todo_list->nr; j++) {
 			struct todo_item *item = &todo_list->items[j];
 			const char *arg = todo_list->buf.buf + item->arg_offset;
 
@@ -4300,7 +4302,7 @@ void todo_list_filter_update_refs(struct repository *r,
 	 * For each todo_item, check if its ref is in the update_refs list.
 	 * If not, then add it as an un-updated ref.
 	 */
-	for (i = 0; i < todo_list->total_nr; i++) {
+	for (i = 0; i < todo_list->nr; i++) {
 		struct todo_item *item = &todo_list->items[i];
 		const char *arg = todo_list->buf.buf + item->arg_offset;
 		int j, found = 0;
@@ -6148,7 +6150,8 @@ int complete_action(struct repository *r, struct replay_opts *opts, unsigned fla
 	todo_list_to_strbuf(r, &new_todo, &buf2, -1, 0);
 	strbuf_swap(&new_todo.buf, &buf2);
 	strbuf_release(&buf2);
-	new_todo.total_nr -= new_todo.nr;
+	/* Nothing is done yet, and we're reparsing, so let's reset the count */
+	new_todo.total_nr = 0;
 	if (todo_list_parse_insn_buffer(r, new_todo.buf.buf, &new_todo) < 0)
 		BUG("invalid todo list after expanding IDs:\n%s",
 		    new_todo.buf.buf);
diff --git a/t/lib-submodule-update.sh b/t/lib-submodule-update.sh
index dee14992c52d5d..9acb0d5d19d2ec 100644
--- a/t/lib-submodule-update.sh
+++ b/t/lib-submodule-update.sh
@@ -802,7 +802,7 @@ test_submodule_recursing_with_args_common () {
 			git branch -t no_submodule origin/no_submodule &&
 			$command no_submodule &&
 			test_superproject_content origin/no_submodule &&
-			! test_path_is_dir sub1 &&
+			test_path_is_missing sub1 &&
 			test_must_fail git config -f .git/modules/sub1/config core.worktree &&
 			test_must_fail git config -f .git/modules/sub1/modules/sub2/config core.worktree
 		)
diff --git a/t/t1092-sparse-checkout-compatibility.sh b/t/t1092-sparse-checkout-compatibility.sh
index e58bfbfcb4f385..a63d0cc222102b 100755
--- a/t/t1092-sparse-checkout-compatibility.sh
+++ b/t/t1092-sparse-checkout-compatibility.sh
@@ -2089,22 +2089,32 @@ test_expect_success 'grep sparse directory within submodules' '
 	test_cmp actual expect
 '
 
-test_expect_success 'write-tree on all' '
+test_expect_success 'write-tree' '
 	init_repos &&
 
+	test_all_match git write-tree &&
+
 	write_script edit-contents <<-\EOF &&
 	echo text >>"$1"
 	EOF
 
+	# make a change inside the sparse cone
 	run_on_all ../edit-contents deep/a &&
-	run_on_all git update-index deep/a &&
+	test_all_match git update-index deep/a &&
 	test_all_match git write-tree &&
+	test_all_match git status --porcelain=v2 &&
 
+	# make a change outside the sparse cone
 	run_on_all mkdir -p folder1 &&
 	run_on_all cp a folder1/a &&
 	run_on_all ../edit-contents folder1/a &&
-	run_on_all git update-index folder1/a &&
-	test_all_match git write-tree
+	test_all_match git update-index folder1/a &&
+	test_all_match git write-tree &&
+	test_all_match git status --porcelain=v2 &&
+
+	# check that SKIP_WORKTREE files are not materialized
+	test_path_is_missing sparse-checkout/folder2/a &&
+	test_path_is_missing sparse-index/folder2/a
 '
 
 test_expect_success 'sparse-index is not expanded: write-tree' '
diff --git a/t/t2021-checkout-overwrite.sh b/t/t2021-checkout-overwrite.sh
index 034f62c13c5949..ecfacf0f7f3a5f 100755
--- a/t/t2021-checkout-overwrite.sh
+++ b/t/t2021-checkout-overwrite.sh
@@ -77,7 +77,7 @@ test_expect_success 'checkout --overwrite-ignore should succeed if only ignored
 	echo autogenerated information >some_dir/ignore &&
 	echo ignore >.git/info/exclude &&
 	git checkout --overwrite-ignore df_conflict &&
-	! test_path_is_dir some_dir
+	test_path_is_file some_dir
 '
 
 test_done
diff --git a/t/t3430-rebase-merges.sh b/t/t3430-rebase-merges.sh
index f03599c63b969d..96ae0edf1e1727 100755
--- a/t/t3430-rebase-merges.sh
+++ b/t/t3430-rebase-merges.sh
@@ -578,4 +578,12 @@ test_expect_success '--rebase-merges with message matched with onto label' '
 	EOF
 '
 
+test_expect_success 'progress shows the correct total' '
+	git checkout -b progress H &&
+	git rebase --rebase-merges --force-rebase --verbose A 2> err &&
+	# Expecting "Rebasing (N/14)" here, no bogus total number
+	grep "^Rebasing.*/14.$" err >progress &&
+	test_line_count = 14 progress
+'
+
 test_done
diff --git a/t/t4067-diff-partial-clone.sh b/t/t4067-diff-partial-clone.sh
index f60f5cbd65f049..7af3a08862dec8 100755
--- a/t/t4067-diff-partial-clone.sh
+++ b/t/t4067-diff-partial-clone.sh
@@ -151,7 +151,7 @@ test_expect_success 'diff does not fetch anything if inexact rename detection is
 
 	# Ensure no fetches.
 	GIT_TRACE_PACKET="$(pwd)/trace" git -C client diff --raw -M HEAD^ HEAD &&
-	! test_path_exists trace
+	test_path_is_missing trace
 '
 
 test_expect_success 'diff --break-rewrites fetches only if necessary, and batches blobs if it does' '
@@ -171,7 +171,7 @@ test_expect_success 'diff --break-rewrites fetches only if necessary, and batche
 
 	# Ensure no fetches.
 	GIT_TRACE_PACKET="$(pwd)/trace" git -C client diff --raw -M HEAD^ HEAD &&
-	! test_path_exists trace &&
+	test_path_is_missing trace &&
 
 	# But with --break-rewrites, ensure that there is exactly 1 negotiation
 	# by checking that there is only 1 "done" line sent. ("done" marks the
diff --git a/t/t4115-apply-symlink.sh b/t/t4115-apply-symlink.sh
index e95e6d4e7d6419..a22a90d552a8ac 100755
--- a/t/t4115-apply-symlink.sh
+++ b/t/t4115-apply-symlink.sh
@@ -74,7 +74,7 @@ test_expect_success SYMLINKS 'symlink escape when creating new files' '
 	error: affected file ${SQ}renamed-symlink/create-me${SQ} is beyond a symbolic link
 	EOF
 	test_cmp expected_stderr stderr &&
-	! test_path_exists .git/create-me
+	test_path_is_missing .git/create-me
 '
 
 test_expect_success SYMLINKS 'symlink escape when modifying file' '
diff --git a/t/t5572-pull-submodule.sh b/t/t5572-pull-submodule.sh
index 09097eff3f4603..4e917bf87d2d42 100755
--- a/t/t5572-pull-submodule.sh
+++ b/t/t5572-pull-submodule.sh
@@ -121,7 +121,7 @@ test_expect_success "fetch.recurseSubmodules option triggers recursive fetch (bu
 	sub_oid=$(git -C child rev-parse HEAD) &&
 	git -C super/sub cat-file -e $sub_oid &&
 	# Check that the submodule worktree did not update
-	! test_path_is_file super/sub/merge_strategy_5.t
+	test_path_is_missing super/sub/merge_strategy_5.t
 '
 
 test_expect_success "fetch.recurseSubmodules takes precedence over submodule.recurse" '
@@ -134,7 +134,7 @@ test_expect_success "fetch.recurseSubmodules takes precedence over submodule.rec
 	sub_oid=$(git -C child rev-parse HEAD) &&
 	git -C super/sub cat-file -e $sub_oid &&
 	# Check that the submodule worktree did not update
-	! test_path_is_file super/sub/merge_strategy_6.t
+	test_path_is_missing super/sub/merge_strategy_6.t
 '
 
 test_expect_success 'pull --rebase --recurse-submodules (remote superproject submodule changes, local submodule changes)' '