diff --git a/Documentation/config/push.txt b/Documentation/config/push.txt
index 0a0e000..dffd4d5 100644
--- a/Documentation/config/push.txt
+++ b/Documentation/config/push.txt
@@ -79,7 +79,7 @@
 repository) to clear the values inherited from a lower priority
 configuration files (e.g. `$HOME/.gitconfig`).
 +
---
+----
 
 Example:
 
@@ -96,7 +96,7 @@
 
 This will result in only b (a and c are cleared).
 
---
+----
 
 push.recurseSubmodules::
 	Make sure all submodule commits used by the revisions to be pushed
diff --git a/Documentation/doc-diff b/Documentation/doc-diff
index 88a9b20..1694300 100755
--- a/Documentation/doc-diff
+++ b/Documentation/doc-diff
@@ -127,7 +127,7 @@
 	while read src
 	do
 		dst=$2/${src#$1/}
-		printf 'all:: %s\n' "$dst"
+		printf 'all: %s\n' "$dst"
 		printf '%s: %s\n' "$dst" "$src"
 		printf '\t@echo >&2 "  RENDER $(notdir $@)" && \\\n'
 		printf '\tmkdir -p $(dir $@) && \\\n'
diff --git a/Documentation/git-check-ignore.txt b/Documentation/git-check-ignore.txt
index 8b2d49c..0c3924a 100644
--- a/Documentation/git-check-ignore.txt
+++ b/Documentation/git-check-ignore.txt
@@ -30,9 +30,15 @@
 	valid with a single pathname.
 
 -v, --verbose::
-	Also output details about the matching pattern (if any)
-	for each given pathname. For precedence rules within and
-	between exclude sources, see linkgit:gitignore[5].
+	Instead of printing the paths that are excluded, for each path
+	that matches an exclude pattern, print the exclude pattern
+	together with the path.  (Matching an exclude pattern usually
+	means the path is excluded, but if the pattern begins with '!'
+	then it is a negated pattern and matching it means the path is
+	NOT excluded.)
++
+For precedence rules within and between exclude sources, see
+linkgit:gitignore[5].
 
 --stdin::
 	Read pathnames from the standard input, one per line,
diff --git a/add-interactive.c b/add-interactive.c
index 6a5048c..143e694 100644
--- a/add-interactive.c
+++ b/add-interactive.c
@@ -326,7 +326,10 @@
 				if (endp == p + sep)
 					to = from + 1;
 				else if (*endp == '-') {
-					to = strtoul(++endp, &endp, 10);
+					if (isdigit(*(++endp)))
+						to = strtoul(endp, &endp, 10);
+					else
+						to = items->items.nr;
 					/* extra characters after the range? */
 					if (endp != p + sep)
 						from = -1;
@@ -913,7 +916,7 @@
 
 	opts->prompt = N_("Patch update");
 	count = list_and_choose(s, files, opts);
-	if (count >= 0) {
+	if (count > 0) {
 		struct argv_array args = ARGV_ARRAY_INIT;
 		struct pathspec ps_selected = { 0 };
 
@@ -954,7 +957,7 @@
 	opts->flags = IMMEDIATE;
 	count = list_and_choose(s, files, opts);
 	opts->flags = 0;
-	if (count >= 0) {
+	if (count > 0) {
 		struct argv_array args = ARGV_ARRAY_INIT;
 
 		argv_array_pushl(&args, "git", "diff", "-p", "--cached",
diff --git a/builtin/check-ignore.c b/builtin/check-ignore.c
index 5a4f923..ea5d0ae 100644
--- a/builtin/check-ignore.c
+++ b/builtin/check-ignore.c
@@ -108,6 +108,9 @@
 			int dtype = DT_UNKNOWN;
 			pattern = last_matching_pattern(dir, &the_index,
 							full_path, &dtype);
+			if (!verbose && pattern &&
+			    pattern->flags & PATTERN_FLAG_NEGATIVE)
+				pattern = NULL;
 		}
 		if (!quiet && (pattern || show_non_matching))
 			output_pattern(pathspec.items[i].original, pattern);
diff --git a/builtin/index-pack.c b/builtin/index-pack.c
index 60a5591..41a7c11 100644
--- a/builtin/index-pack.c
+++ b/builtin/index-pack.c
@@ -1003,7 +1003,9 @@
 
 		if (!compare_and_swap_type(&child->real_type, OBJ_REF_DELTA,
 					   base->obj->real_type))
-			BUG("child->real_type != OBJ_REF_DELTA");
+			die("REF_DELTA at offset %"PRIuMAX" already resolved (duplicate base %s?)",
+			    (uintmax_t)child->idx.offset,
+			    oid_to_hex(&base->obj->idx.oid));
 
 		resolve_delta(child, base, result);
 		if (base->ref_first == base->ref_last && base->ofs_last == -1)
diff --git a/compat/obstack.h b/compat/obstack.h
index 01e7c81..f90a46d 100644
--- a/compat/obstack.h
+++ b/compat/obstack.h
@@ -135,8 +135,10 @@
    alignment relative to 0.  */
 
 #define __PTR_ALIGN(B, P, A)						    \
-  __BPTR_ALIGN (sizeof (PTR_INT_TYPE) < sizeof (void *) ? (B) : (char *) 0, \
-		P, A)
+  (sizeof (PTR_INT_TYPE) < sizeof(void *) ?                                 \
+   __BPTR_ALIGN((B), (P), (A)) :                                            \
+   (void *)__BPTR_ALIGN((PTR_INT_TYPE)(void *)0, (PTR_INT_TYPE)(P), (A))            \
+  )
 
 #include <string.h>
 
diff --git a/merge-recursive.c b/merge-recursive.c
index 9657adc..e6f943c 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -1715,6 +1715,14 @@
 	return new_path;
 }
 
+/*
+ * Toggle the stage number between "ours" and "theirs" (2 and 3).
+ */
+static inline int flip_stage(int stage)
+{
+	return (2 + 3) - stage;
+}
+
 static int handle_rename_rename_1to2(struct merge_options *opt,
 				     struct rename_conflict_info *ci)
 {
@@ -1759,14 +1767,14 @@
 		 * such cases, we should keep the added file around,
 		 * resolving the conflict at that path in its favor.
 		 */
-		add = &ci->ren1->dst_entry->stages[2 ^ 1];
+		add = &ci->ren1->dst_entry->stages[flip_stage(2)];
 		if (is_valid(add)) {
 			if (update_file(opt, 0, add, a->path))
 				return -1;
 		}
 		else
 			remove_file_from_index(opt->repo->index, a->path);
-		add = &ci->ren2->dst_entry->stages[3 ^ 1];
+		add = &ci->ren2->dst_entry->stages[flip_stage(3)];
 		if (is_valid(add)) {
 			if (update_file(opt, 0, add, b->path))
 				return -1;
@@ -1779,7 +1787,7 @@
 		 * rename/add collision.  If not, we can write the file out
 		 * to the specified location.
 		 */
-		add = &ci->ren1->dst_entry->stages[2 ^ 1];
+		add = &ci->ren1->dst_entry->stages[flip_stage(2)];
 		if (is_valid(add)) {
 			add->path = mfi.blob.path = a->path;
 			if (handle_file_collision(opt, a->path,
@@ -1800,7 +1808,7 @@
 				return -1;
 		}
 
-		add = &ci->ren2->dst_entry->stages[3 ^ 1];
+		add = &ci->ren2->dst_entry->stages[flip_stage(3)];
 		if (is_valid(add)) {
 			add->path = mfi.blob.path = b->path;
 			if (handle_file_collision(opt, b->path,
@@ -1849,7 +1857,7 @@
 	path_side_1_desc = xstrfmt("version of %s from %s", path, a->path);
 	path_side_2_desc = xstrfmt("version of %s from %s", path, b->path);
 	ostage1 = ci->ren1->branch == opt->branch1 ? 3 : 2;
-	ostage2 = ostage1 ^ 1;
+	ostage2 = flip_stage(ostage1);
 	ci->ren1->src_entry->stages[ostage1].path = a->path;
 	ci->ren2->src_entry->stages[ostage2].path = b->path;
 	if (merge_mode_and_contents(opt, a, c1,
diff --git a/notes.c b/notes.c
index 0c79964..2de7f4b 100644
--- a/notes.c
+++ b/notes.c
@@ -576,16 +576,16 @@
 			 * the note tree that have not yet been explored. There
 			 * is a direct relationship between subtree entries at
 			 * level 'n' in the tree, and the 'fanout' variable:
-			 * Subtree entries at level 'n <= 2 * fanout' should be
+			 * Subtree entries at level 'n < 2 * fanout' should be
 			 * preserved, since they correspond exactly to a fanout
 			 * directory in the on-disk structure. However, subtree
-			 * entries at level 'n > 2 * fanout' should NOT be
+			 * entries at level 'n >= 2 * fanout' should NOT be
 			 * preserved, but rather consolidated into the above
 			 * notes tree level. We achieve this by unconditionally
 			 * unpacking subtree entries that exist below the
 			 * threshold level at 'n = 2 * fanout'.
 			 */
-			if (n <= 2 * fanout &&
+			if (n < 2 * fanout &&
 			    flags & FOR_EACH_NOTE_YIELD_SUBTREES) {
 				/* invoke callback with subtree */
 				unsigned int path_len =
@@ -602,7 +602,7 @@
 					 path,
 					 cb_data);
 			}
-			if (n > fanout * 2 ||
+			if (n >= 2 * fanout ||
 			    !(flags & FOR_EACH_NOTE_DONT_UNPACK_SUBTREES)) {
 				/* unpack subtree and resume traversal */
 				tree->a[i] = NULL;
@@ -723,13 +723,15 @@
 
 struct write_each_note_data {
 	struct tree_write_stack *root;
-	struct non_note *next_non_note;
+	struct non_note **nn_list;
+	struct non_note *nn_prev;
 };
 
 static int write_each_non_note_until(const char *note_path,
 		struct write_each_note_data *d)
 {
-	struct non_note *n = d->next_non_note;
+	struct non_note *p = d->nn_prev;
+	struct non_note *n = p ? p->next : *d->nn_list;
 	int cmp = 0, ret;
 	while (n && (!note_path || (cmp = strcmp(n->path, note_path)) <= 0)) {
 		if (note_path && cmp == 0)
@@ -740,9 +742,10 @@
 			if (ret)
 				return ret;
 		}
+		p = n;
 		n = n->next;
 	}
-	d->next_non_note = n;
+	d->nn_prev = p;
 	return 0;
 }
 
@@ -1177,7 +1180,8 @@
 	strbuf_init(&root.buf, 256 * (32 + the_hash_algo->hexsz)); /* assume 256 entries */
 	root.path[0] = root.path[1] = '\0';
 	cb_data.root = &root;
-	cb_data.next_non_note = t->first_non_note;
+	cb_data.nn_list = &(t->first_non_note);
+	cb_data.nn_prev = NULL;
 
 	/* Write tree objects representing current notes tree */
 	flags = FOR_EACH_NOTE_DONT_UNPACK_SUBTREES |
diff --git a/pathspec.c b/pathspec.c
index 128f27f..8243e06 100644
--- a/pathspec.c
+++ b/pathspec.c
@@ -438,8 +438,13 @@
 	} else {
 		match = prefix_path_gently(prefix, prefixlen,
 					   &prefixlen, copyfrom);
-		if (!match)
-			die(_("%s: '%s' is outside repository"), elt, copyfrom);
+		if (!match) {
+			const char *hint_path = get_git_work_tree();
+			if (!hint_path)
+				hint_path = get_git_dir();
+			die(_("%s: '%s' is outside repository at '%s'"), elt,
+			    copyfrom, absolute_path(hint_path));
+		}
 	}
 
 	item->match = match;
diff --git a/rebase-interactive.c b/rebase-interactive.c
index aa18ae8..1259adc 100644
--- a/rebase-interactive.c
+++ b/rebase-interactive.c
@@ -104,9 +104,11 @@
 				    -1, flags | TODO_LIST_SHORTEN_IDS | TODO_LIST_APPEND_TODO_HELP))
 		return error_errno(_("could not write '%s'"), todo_file);
 
-	if (initial && copy_file(rebase_path_todo_backup(), todo_file, 0666))
-		return error(_("could not copy '%s' to '%s'."), todo_file,
-			     rebase_path_todo_backup());
+	if (initial &&
+	    todo_list_write_to_file(r, todo_list, rebase_path_todo_backup(),
+				    shortrevisions, shortonto, -1,
+				    (flags | TODO_LIST_APPEND_TODO_HELP) & ~TODO_LIST_SHORTEN_IDS) < 0)
+		return error(_("could not write '%s'."), rebase_path_todo_backup());
 
 	if (launch_sequence_editor(todo_file, &new_todo->buf, NULL))
 		return -2;
diff --git a/sequencer.c b/sequencer.c
index b9dbf1a..df6d18f 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -588,7 +588,7 @@
 	struct merge_options o;
 	struct tree *next_tree, *base_tree, *head_tree;
 	int clean;
-	char **xopt;
+	int i;
 	struct lock_file index_lock = LOCK_INIT;
 
 	if (repo_hold_locked_index(r, &index_lock, LOCK_REPORT_ON_ERROR) < 0)
@@ -608,8 +608,8 @@
 	next_tree = next ? get_commit_tree(next) : empty_tree(r);
 	base_tree = base ? get_commit_tree(base) : empty_tree(r);
 
-	for (xopt = opts->xopts; xopt != opts->xopts + opts->xopts_nr; xopt++)
-		parse_merge_opt(&o, *xopt);
+	for (i = 0; i < opts->xopts_nr; i++)
+		parse_merge_opt(&o, opts->xopts[i]);
 
 	clean = merge_trees(&o,
 			    head_tree,
@@ -2118,6 +2118,8 @@
 	saved = *end_of_object_name;
 	*end_of_object_name = '\0';
 	status = get_oid(bol, &commit_oid);
+	if (status < 0)
+		error(_("could not parse '%s'"), bol); /* return later */
 	*end_of_object_name = saved;
 
 	bol = end_of_object_name + strspn(end_of_object_name, " \t");
@@ -2125,11 +2127,10 @@
 	item->arg_len = (int)(eol - bol);
 
 	if (status < 0)
-		return error(_("could not parse '%.*s'"),
-			     (int)(end_of_object_name - bol), bol);
+		return status;
 
 	item->commit = lookup_commit_reference(r, &commit_oid);
-	return !item->commit;
+	return item->commit ? 0 : -1;
 }
 
 int sequencer_get_last_command(struct repository *r, enum replay_action *action)
@@ -5075,7 +5076,7 @@
 {
 	const char *shortonto, *todo_file = rebase_path_todo();
 	struct todo_list new_todo = TODO_LIST_INIT;
-	struct strbuf *buf = &todo_list->buf;
+	struct strbuf *buf = &todo_list->buf, buf2 = STRBUF_INIT;
 	struct object_id oid = onto->object.oid;
 	int res;
 
@@ -5127,6 +5128,15 @@
 		return -1;
 	}
 
+	/* Expand the commit IDs */
+	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;
+	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);
+
 	if (opts->allow_ff && skip_unnecessary_picks(r, &new_todo, &oid)) {
 		todo_list_release(&new_todo);
 		return error(_("could not skip unnecessary pick commands"));
diff --git a/setup.c b/setup.c
index e2a479a..f489728 100644
--- a/setup.c
+++ b/setup.c
@@ -120,8 +120,13 @@
 char *prefix_path(const char *prefix, int len, const char *path)
 {
 	char *r = prefix_path_gently(prefix, len, NULL, path);
-	if (!r)
-		die(_("'%s' is outside repository"), path);
+	if (!r) {
+		const char *hint_path = get_git_work_tree();
+		if (!hint_path)
+			hint_path = get_git_dir();
+		die(_("'%s' is outside repository at '%s'"), path,
+		    absolute_path(hint_path));
+	}
 	return r;
 }
 
diff --git a/submodule.c b/submodule.c
index 6b86744..9f4c4c0 100644
--- a/submodule.c
+++ b/submodule.c
@@ -82,7 +82,7 @@
 	if ((pos >= 0) && (pos < istate->cache_nr)) {
 		struct stat st;
 		if (lstat(GITMODULES_FILE, &st) == 0 &&
-		    ie_match_stat(istate, istate->cache[pos], &st, 0) & DATA_CHANGED)
+		    ie_modified(istate, istate->cache[pos], &st, 0) & DATA_CHANGED)
 			return 0;
 	}
 
@@ -1811,7 +1811,7 @@
 void submodule_unset_core_worktree(const struct submodule *sub)
 {
 	char *config_path = xstrfmt("%s/modules/%s/config",
-				    get_git_common_dir(), sub->name);
+				    get_git_dir(), sub->name);
 
 	if (git_config_set_in_file_gently(config_path, "core.worktree", NULL))
 		warning(_("Could not unset core.worktree setting in submodule '%s'"),
@@ -1914,7 +1914,7 @@
 					ABSORB_GITDIR_RECURSE_SUBMODULES);
 		} else {
 			char *gitdir = xstrfmt("%s/modules/%s",
-				    get_git_common_dir(), sub->name);
+				    get_git_dir(), sub->name);
 			connect_work_tree_and_git_dir(path, gitdir, 0);
 			free(gitdir);
 
@@ -1924,7 +1924,7 @@
 
 		if (old_head && (flags & SUBMODULE_MOVE_HEAD_FORCE)) {
 			char *gitdir = xstrfmt("%s/modules/%s",
-				    get_git_common_dir(), sub->name);
+				    get_git_dir(), sub->name);
 			connect_work_tree_and_git_dir(path, gitdir, 1);
 			free(gitdir);
 		}
diff --git a/t/t0008-ignores.sh b/t/t0008-ignores.sh
index 1744cee..370a389 100755
--- a/t/t0008-ignores.sh
+++ b/t/t0008-ignores.sh
@@ -424,9 +424,24 @@
 	)
 '
 
-test_expect_success_multi 'nested include' \
-	'a/b/.gitignore:8:!on*	a/b/one' '
-	test_check_ignore "a/b/one"
+test_expect_success 'nested include of negated pattern' '
+	expect "" &&
+	test_check_ignore "a/b/one" 1
+'
+
+test_expect_success 'nested include of negated pattern with -q' '
+	expect "" &&
+	test_check_ignore "-q a/b/one" 1
+'
+
+test_expect_success 'nested include of negated pattern with -v' '
+	expect "a/b/.gitignore:8:!on*	a/b/one" &&
+	test_check_ignore "-v a/b/one" 0
+'
+
+test_expect_success 'nested include of negated pattern with -v -n' '
+	expect "a/b/.gitignore:8:!on*	a/b/one" &&
+	test_check_ignore "-v -n a/b/one" 0
 '
 
 ############################################################################
@@ -460,7 +475,6 @@
 	expect_from_stdin <<-\EOF &&
 		foo
 		twoooo
-		../one
 		seven
 		../../one
 	EOF
@@ -543,7 +557,6 @@
 		globalthree
 		a/globalthree
 		a/per-repo
-		globaltwo
 	EOF
 	test_check_ignore "globalone per-repo globalthree a/globalthree a/per-repo not-ignored globaltwo"
 '
@@ -586,17 +599,7 @@
 cat <<-\EOF >expected-default
 	one
 	a/one
-	a/b/on
-	a/b/one
-	a/b/one one
-	a/b/one two
-	"a/b/one\"three"
-	a/b/two
 	a/b/twooo
-	globaltwo
-	a/globaltwo
-	a/b/globaltwo
-	b/globaltwo
 EOF
 cat <<-EOF >expected-verbose
 	.gitignore:1:one	one
@@ -696,8 +699,12 @@
 	$global_excludes:2:!globaltwo	../b/globaltwo
 	::	c/not-ignored
 EOF
+cat <<-EOF >expected-default
+../one
+one
+b/twooo
+EOF
 grep -v '^::	' expected-all >expected-verbose
-sed -e 's/.*	//' expected-verbose >expected-default
 
 broken_c_unquote stdin >stdin0
 
diff --git a/t/t2405-worktree-submodule.sh b/t/t2405-worktree-submodule.sh
new file mode 100755
index 0000000..e1b2bfd
--- /dev/null
+++ b/t/t2405-worktree-submodule.sh
@@ -0,0 +1,90 @@
+#!/bin/sh
+
+test_description='Combination of submodules and multiple worktrees'
+
+. ./test-lib.sh
+
+base_path=$(pwd -P)
+
+test_expect_success 'setup: create origin repos'  '
+	git init origin/sub &&
+	test_commit -C origin/sub file1 &&
+	git init origin/main &&
+	test_commit -C origin/main first &&
+	git -C origin/main submodule add ../sub &&
+	git -C origin/main commit -m "add sub" &&
+	test_commit -C origin/sub "file1 updated" file1 file1updated file1updated &&
+	git -C origin/main/sub pull &&
+	git -C origin/main add sub &&
+	git -C origin/main commit -m "sub updated"
+'
+
+test_expect_success 'setup: clone superproject to create main worktree' '
+	git clone --recursive "$base_path/origin/main" main
+'
+
+rev1_hash_main=$(git --git-dir=origin/main/.git show --pretty=format:%h -q "HEAD~1")
+rev1_hash_sub=$(git --git-dir=origin/sub/.git show --pretty=format:%h -q "HEAD~1")
+
+test_expect_success 'add superproject worktree' '
+	git -C main worktree add "$base_path/worktree" "$rev1_hash_main"
+'
+
+test_expect_failure 'submodule is checked out just after worktree add' '
+	git -C worktree diff --submodule master"^!" >out &&
+	grep "file1 updated" out
+'
+
+test_expect_success 'add superproject worktree and initialize submodules' '
+	git -C main worktree add "$base_path/worktree-submodule-update" "$rev1_hash_main" &&
+	git -C worktree-submodule-update submodule update
+'
+
+test_expect_success 'submodule is checked out just after submodule update in linked worktree' '
+	git -C worktree-submodule-update diff --submodule master"^!" >out &&
+	grep "file1 updated" out
+'
+
+test_expect_success 'add superproject worktree and manually add submodule worktree' '
+	git -C main worktree add "$base_path/linked_submodule" "$rev1_hash_main" &&
+	git -C main/sub worktree add "$base_path/linked_submodule/sub" "$rev1_hash_sub"
+'
+
+test_expect_success 'submodule is checked out after manually adding submodule worktree' '
+	git -C linked_submodule diff --submodule master"^!" >out &&
+	grep "file1 updated" out
+'
+
+test_expect_success 'checkout --recurse-submodules uses $GIT_DIR for submodules in a linked worktree' '
+	git -C main worktree add "$base_path/checkout-recurse" --detach  &&
+	git -C checkout-recurse submodule update --init &&
+	echo "gitdir: ../../main/.git/worktrees/checkout-recurse/modules/sub" >expect-gitfile &&
+	cat checkout-recurse/sub/.git >actual-gitfile &&
+	test_cmp expect-gitfile actual-gitfile &&
+	git -C main/sub rev-parse HEAD >expect-head-main &&
+	git -C checkout-recurse checkout --recurse-submodules HEAD~1 &&
+	cat checkout-recurse/sub/.git >actual-gitfile &&
+	git -C main/sub rev-parse HEAD >actual-head-main &&
+	test_cmp expect-gitfile actual-gitfile &&
+	test_cmp expect-head-main actual-head-main
+'
+
+test_expect_success 'core.worktree is removed in $GIT_DIR/modules/<name>/config, not in $GIT_COMMON_DIR/modules/<name>/config' '
+	echo "../../../sub" >expect-main &&
+	git -C main/sub config --get core.worktree >actual-main &&
+	test_cmp expect-main actual-main &&
+	echo "../../../../../../checkout-recurse/sub" >expect-linked &&
+	git -C checkout-recurse/sub config --get core.worktree >actual-linked &&
+	test_cmp expect-linked actual-linked &&
+	git -C checkout-recurse checkout --recurse-submodules first &&
+	test_expect_code 1 git -C main/.git/worktrees/checkout-recurse/modules/sub config --get core.worktree >linked-config &&
+	test_must_be_empty linked-config &&
+	git -C main/sub config --get core.worktree >actual-main &&
+	test_cmp expect-main actual-main
+'
+
+test_expect_success 'unsetting core.worktree does not prevent running commands directly against the submodule repository' '
+	git -C main/.git/worktrees/checkout-recurse/modules/sub log
+'
+
+test_done
diff --git a/t/t3305-notes-fanout.sh b/t/t3305-notes-fanout.sh
index 831f83d..3b4753e 100755
--- a/t/t3305-notes-fanout.sh
+++ b/t/t3305-notes-fanout.sh
@@ -4,6 +4,38 @@
 
 . ./test-lib.sh
 
+path_has_fanout() {
+	path=$1 &&
+	fanout=$2 &&
+	after_last_slash=$((40 - $fanout * 2)) &&
+	echo $path | grep -q "^\([0-9a-f]\{2\}/\)\{$fanout\}[0-9a-f]\{$after_last_slash\}$"
+}
+
+touched_one_note_with_fanout() {
+	notes_commit=$1 &&
+	modification=$2 &&  # 'A' for addition, 'D' for deletion
+	fanout=$3 &&
+	diff=$(git diff-tree --no-commit-id --name-status --root -r $notes_commit) &&
+	path=$(echo $diff | sed -e "s/^$modification[\t ]//") &&
+	path_has_fanout "$path" $fanout;
+}
+
+all_notes_have_fanout() {
+	notes_commit=$1 &&
+	fanout=$2 &&
+	git ls-tree -r --name-only $notes_commit 2>/dev/null |
+	while read path
+	do
+		path_has_fanout $path $fanout || return 1
+	done
+}
+
+test_expect_success 'tweak test environment' '
+	git checkout -b nondeterminism &&
+	test_commit A &&
+	git checkout --orphan with_notes;
+'
+
 test_expect_success 'creating many notes with git-notes' '
 	num_notes=300 &&
 	i=0 &&
@@ -20,7 +52,7 @@
 
 test_expect_success 'many notes created correctly with git-notes' '
 	git log | grep "^    " > output &&
-	i=300 &&
+	i=$num_notes &&
 	while test $i -gt 0
 	do
 		echo "    commit #$i" &&
@@ -30,34 +62,46 @@
 	test_cmp expect output
 '
 
-test_expect_success 'many notes created with git-notes triggers fanout' '
-	# Expect entire notes tree to have a fanout == 1
-	git ls-tree -r --name-only refs/notes/commits |
-	while read path
+test_expect_success 'stable fanout 0 is followed by stable fanout 1' '
+	i=$num_notes &&
+	fanout=0 &&
+	while test $i -gt 0
 	do
-		echo $path | grep "^../[0-9a-f]*$" || {
-			echo "Invalid path \"$path\"" &&
-			return 1;
-		}
-	done
+		i=$(($i - 1)) &&
+		if touched_one_note_with_fanout refs/notes/commits~$i A $fanout
+		then
+			continue
+		elif test $fanout -eq 0
+		then
+			fanout=1 &&
+			if all_notes_have_fanout refs/notes/commits~$i $fanout
+			then
+				echo "Fanout 0 -> 1 at refs/notes/commits~$i" &&
+				continue
+			fi
+		fi &&
+		echo "Failed fanout=$fanout check at refs/notes/commits~$i" &&
+		git ls-tree -r --name-only refs/notes/commits~$i &&
+		return 1
+	done &&
+	all_notes_have_fanout refs/notes/commits 1
 '
 
 test_expect_success 'deleting most notes with git-notes' '
-	num_notes=250 &&
+	remove_notes=285 &&
 	i=0 &&
 	git rev-list HEAD |
-	while test $i -lt $num_notes && read sha1
+	while test $i -lt $remove_notes && read sha1
 	do
 		i=$(($i + 1)) &&
 		test_tick &&
-		git notes remove "$sha1" ||
-		exit 1
+		git notes remove "$sha1" 2>/dev/null || return 1
 	done
 '
 
 test_expect_success 'most notes deleted correctly with git-notes' '
-	git log HEAD~250 | grep "^    " > output &&
-	i=50 &&
+	git log HEAD~$remove_notes | grep "^    " > output &&
+	i=$(($num_notes - $remove_notes)) &&
 	while test $i -gt 0
 	do
 		echo "    commit #$i" &&
@@ -67,16 +111,29 @@
 	test_cmp expect output
 '
 
-test_expect_success 'deleting most notes triggers fanout consolidation' '
-	# Expect entire notes tree to have a fanout == 0
-	git ls-tree -r --name-only refs/notes/commits |
-	while read path
+test_expect_success 'stable fanout 1 is followed by stable fanout 0' '
+	i=$remove_notes &&
+	fanout=1 &&
+	while test $i -gt 0
 	do
-		echo $path | grep -v "^../.*" || {
-			echo "Invalid path \"$path\"" &&
-			return 1;
-		}
-	done
+		i=$(($i - 1)) &&
+		if touched_one_note_with_fanout refs/notes/commits~$i D $fanout
+		then
+			continue
+		elif test $fanout -eq 1
+		then
+			fanout=0 &&
+			if all_notes_have_fanout refs/notes/commits~$i $fanout
+			then
+				echo "Fanout 1 -> 0 at refs/notes/commits~$i" &&
+				continue
+			fi
+		fi &&
+		echo "Failed fanout=$fanout check at refs/notes/commits~$i" &&
+		git ls-tree -r --name-only refs/notes/commits~$i &&
+		return 1
+	done &&
+	all_notes_have_fanout refs/notes/commits 0
 '
 
 test_done
diff --git a/t/t3404-rebase-interactive.sh b/t/t3404-rebase-interactive.sh
index ae6e55c..b90ea0f 100755
--- a/t/t3404-rebase-interactive.sh
+++ b/t/t3404-rebase-interactive.sh
@@ -1264,13 +1264,26 @@
 test_expect_success SHA1 'short SHA-1 collide' '
 	test_when_finished "reset_rebase && git checkout master" &&
 	git checkout collide &&
+	colliding_sha1=6bcda37 &&
+	test $colliding_sha1 = "$(git rev-parse HEAD | cut -c 1-7)" &&
 	(
 		unset test_tick &&
 		test_tick &&
 		set_fake_editor &&
 		FAKE_COMMIT_MESSAGE="collide2 ac4f2ee" \
-		FAKE_LINES="reword 1 2" git rebase -i HEAD~2
-	)
+		FAKE_LINES="reword 1 break 2" git rebase -i HEAD~2 &&
+		test $colliding_sha1 = "$(git rev-parse HEAD | cut -c 1-7)" &&
+		grep "^pick $colliding_sha1 " \
+			.git/rebase-merge/git-rebase-todo.tmp &&
+		grep "^pick [0-9a-f]\{40\}" \
+			.git/rebase-merge/git-rebase-todo &&
+		grep "^pick [0-9a-f]\{40\}" \
+			.git/rebase-merge/git-rebase-todo.backup &&
+		git rebase --continue
+	) &&
+	collide2="$(git rev-parse HEAD~1 | cut -c 1-4)" &&
+	collide3="$(git rev-parse collide3 | cut -c 1-4)" &&
+	test "$collide2" = "$collide3"
 '
 
 test_expect_success 'respect core.abbrev' '
diff --git a/t/t3600-rm.sh b/t/t3600-rm.sh
index 0ea858d..f2c0168 100755
--- a/t/t3600-rm.sh
+++ b/t/t3600-rm.sh
@@ -425,6 +425,13 @@
 	git status -s -uno >actual &&
 	test_cmp expect actual
 '
+test_expect_success 'rm will not error out on .gitmodules file with zero stat data' '
+	git reset --hard &&
+	git submodule update &&
+	git read-tree HEAD &&
+	git rm submod &&
+	test_path_is_missing submod
+'
 
 test_expect_success 'rm issues a warning when section is not found in .gitmodules' '
 	git reset --hard &&
diff --git a/t/t3701-add-interactive.sh b/t/t3701-add-interactive.sh
index 12ee321..2182b1c 100755
--- a/t/t3701-add-interactive.sh
+++ b/t/t3701-add-interactive.sh
@@ -68,6 +68,15 @@
 	! grep . output
 '
 
+test_expect_success 'add untracked (multiple)' '
+	test_when_finished "git reset && rm [1-9]" &&
+	touch $(test_seq 9) &&
+	test_write_lines a "2-5 8-" | git add -i -- [1-9] &&
+	test_write_lines 2 3 4 5 8 9 >expected &&
+	git ls-files [1-9] >output &&
+	test_cmp expected output
+'
+
 test_expect_success 'setup (commit)' '
 	echo baseline >file &&
 	git add file &&
diff --git a/t/t5309-pack-delta-cycles.sh b/t/t5309-pack-delta-cycles.sh
index 491556da..6c209ad 100755
--- a/t/t5309-pack-delta-cycles.sh
+++ b/t/t5309-pack-delta-cycles.sh
@@ -62,13 +62,13 @@
 	test_must_fail git index-pack --fix-thin --stdin <cycle.pack
 '
 
-test_expect_failure 'failover to an object in another pack' '
+test_expect_success 'failover to an object in another pack' '
 	clear_packs &&
 	git index-pack --stdin <ab.pack &&
-	git index-pack --stdin --fix-thin <cycle.pack
+	test_must_fail git index-pack --stdin --fix-thin <cycle.pack
 '
 
-test_expect_failure 'failover to a duplicate object in the same pack' '
+test_expect_success 'failover to a duplicate object in the same pack' '
 	clear_packs &&
 	{
 		pack_header 3 &&
@@ -77,7 +77,7 @@
 		pack_obj $A
 	} >recoverable.pack &&
 	pack_trailer recoverable.pack &&
-	git index-pack --fix-thin --stdin <recoverable.pack
+	test_must_fail git index-pack --fix-thin --stdin <recoverable.pack
 '
 
 test_done
diff --git a/t/t6136-pathspec-in-bare.sh b/t/t6136-pathspec-in-bare.sh
new file mode 100755
index 0000000..b117251
--- /dev/null
+++ b/t/t6136-pathspec-in-bare.sh
@@ -0,0 +1,38 @@
+#!/bin/sh
+
+test_description='diagnosing out-of-scope pathspec'
+
+. ./test-lib.sh
+
+test_expect_success 'setup a bare and non-bare repository' '
+	test_commit file1 &&
+	git clone --bare . bare
+'
+
+test_expect_success 'log and ls-files in a bare repository' '
+	(
+		cd bare &&
+		test_must_fail git log -- .. >out 2>err &&
+		test_must_be_empty out &&
+		test_i18ngrep "outside repository" err &&
+
+		test_must_fail git ls-files -- .. >out 2>err &&
+		test_must_be_empty out &&
+		test_i18ngrep "outside repository" err
+	)
+'
+
+test_expect_success 'log and ls-files in .git directory' '
+	(
+		cd .git &&
+		test_must_fail git log -- .. >out 2>err &&
+		test_must_be_empty out &&
+		test_i18ngrep "outside repository" err &&
+
+		test_must_fail git ls-files -- .. >out 2>err &&
+		test_must_be_empty out &&
+		test_i18ngrep "outside repository" err
+	)
+'
+
+test_done
diff --git a/t/t7410-submodule-checkout-to.sh b/t/t7410-submodule-checkout-to.sh
deleted file mode 100755
index f1b492e..0000000
--- a/t/t7410-submodule-checkout-to.sh
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/bin/sh
-
-test_description='Combination of submodules and multiple workdirs'
-
-. ./test-lib.sh
-
-base_path=$(pwd -P)
-
-test_expect_success 'setup: make origin'  '
-	mkdir -p origin/sub &&
-	(
-		cd origin/sub && git init &&
-		echo file1 >file1 &&
-		git add file1 &&
-		git commit -m file1
-	) &&
-	mkdir -p origin/main &&
-	(
-		cd origin/main && git init &&
-		git submodule add ../sub &&
-		git commit -m "add sub"
-	) &&
-	(
-		cd origin/sub &&
-		echo file1updated >file1 &&
-		git add file1 &&
-		git commit -m "file1 updated"
-	) &&
-	git -C origin/main/sub pull &&
-	(
-		cd origin/main &&
-		git add sub &&
-		git commit -m "sub updated"
-	)
-'
-
-test_expect_success 'setup: clone' '
-	mkdir clone &&
-	git -C clone clone --recursive "$base_path/origin/main"
-'
-
-rev1_hash_main=$(git --git-dir=origin/main/.git show --pretty=format:%h -q "HEAD~1")
-rev1_hash_sub=$(git --git-dir=origin/sub/.git show --pretty=format:%h -q "HEAD~1")
-
-test_expect_success 'checkout main' '
-	mkdir default_checkout &&
-	git -C clone/main worktree add "$base_path/default_checkout/main" "$rev1_hash_main"
-'
-
-test_expect_failure 'can see submodule diffs just after checkout' '
-	git -C default_checkout/main diff --submodule master"^!" >out &&
-	grep "file1 updated" out
-'
-
-test_expect_success 'checkout main and initialize independent clones' '
-	mkdir fully_cloned_submodule &&
-	git -C clone/main worktree add "$base_path/fully_cloned_submodule/main" "$rev1_hash_main" &&
-	git -C fully_cloned_submodule/main submodule update
-'
-
-test_expect_success 'can see submodule diffs after independent cloning' '
-	git -C fully_cloned_submodule/main diff --submodule master"^!" >out &&
-	grep "file1 updated" out
-'
-
-test_expect_success 'checkout sub manually' '
-	mkdir linked_submodule &&
-	git -C clone/main worktree add "$base_path/linked_submodule/main" "$rev1_hash_main" &&
-	git -C clone/main/sub worktree add "$base_path/linked_submodule/main/sub" "$rev1_hash_sub"
-'
-
-test_expect_success 'can see submodule diffs after manual checkout of linked submodule' '
-	git -C linked_submodule/main diff --submodule master"^!" >out &&
-	grep "file1 updated" out
-'
-
-test_done
diff --git a/unpack-trees.c b/unpack-trees.c
index 191e738..70247aa 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -1350,7 +1350,7 @@
 			    enum pattern_match_result default_match,
 			    int progress_nr)
 {
-	struct cache_entry **cache_end = cache + nr;
+	struct cache_entry **cache_end = nr ? cache + nr : cache;
 
 	/*
 	 * Process all entries that have the given prefix and meet
diff --git a/xdiff-interface.c b/xdiff-interface.c
index 8509f9e..4d20069 100644
--- a/xdiff-interface.c
+++ b/xdiff-interface.c
@@ -84,8 +84,8 @@
 {
 	const int blk = 1024;
 	long trimmed = 0, recovered = 0;
-	char *ap = a->ptr + a->size;
-	char *bp = b->ptr + b->size;
+	char *ap = a->size ? a->ptr + a->size : a->ptr;
+	char *bp = b->size ? b->ptr + b->size : b->ptr;
 	long smaller = (a->size < b->size) ? a->size : b->size;
 
 	while (blk + trimmed <= smaller && !memcmp(ap - blk, bp - blk, blk)) {
@@ -250,9 +250,13 @@
 	ALLOC_ARRAY(regs->array, regs->nr);
 	for (i = 0; i < regs->nr; i++) {
 		struct ff_reg *reg = regs->array + i;
-		const char *ep = strchr(value, '\n'), *expression;
+		const char *ep, *expression;
 		char *buffer = NULL;
 
+		if (!value)
+			BUG("mismatch between line count and parsing");
+		ep = strchr(value, '\n');
+
 		reg->negate = (*value == '!');
 		if (reg->negate && i == regs->nr - 1)
 			die("Last expression must not be negated: %s", value);
@@ -265,7 +269,7 @@
 		if (regcomp(&reg->re, expression, cflags))
 			die("Invalid regexp to look for hunk header: %s", expression);
 		free(buffer);
-		value = ep + 1;
+		value = ep ? ep + 1 : NULL;
 	}
 }