diff --git a/Documentation/RelNotes/2.25.1.txt b/Documentation/RelNotes/2.25.1.txt
new file mode 100644
index 0000000..cd869b0
--- /dev/null
+++ b/Documentation/RelNotes/2.25.1.txt
@@ -0,0 +1,55 @@
+Git 2.25.1 Release Notes
+========================
+
+Fixes since v2.25
+-----------------
+
+ * "git commit" gives output similar to "git status" when there is
+   nothing to commit, but without honoring the advise.statusHints
+   configuration variable, which has been corrected.
+
+ * has_object_file() said "no" given an object registered to the
+   system via pretend_object_file(), making it inconsistent with
+   read_object_file(), causing lazy fetch to attempt fetching an
+   empty tree from promisor remotes.
+
+ * The code that tries to skip over the entries for the paths in a
+   single directory using the cache-tree was not careful enough
+   against corrupt index file.
+
+ * Complete an update to tutorial that encourages "git switch" over
+   "git checkout" that was done only half-way.
+
+ * Reduce unnecessary round-trip when running "ls-remote" over the
+   stateless RPC mechanism.
+
+ * "git restore --staged" did not correctly update the cache-tree
+   structure, resulting in bogus trees to be written afterwards, which
+   has been corrected.
+
+ * The code recently added to move to the entry beyond the ones in the
+   same directory in the index in the sparse-cone mode did not count
+   the number of entries to skip over incorrectly, which has been
+   corrected.
+
+ * Work around test breakages caused by custom regex engine used in
+   libasan, when address sanitizer is used with more recent versions
+   of gcc and clang.
+
+ * "git fetch --refmap=" option has got a better documentation.
+
+ * Corner case bugs in "git clean" that stems from a (necessarily for
+   performance reasons) awkward calling convention in the directory
+   enumeration API has been corrected.
+
+ * "git grep --no-index" should not get affected by the contents of
+   the .gitmodules file but when "--recurse-submodules" is given or
+   the "submodule.recurse" variable is set, it did.  Now these
+   settings are ignored in the "--no-index" mode.
+
+ * Technical details of the bundle format has been documented.
+
+ * Unhelpful warning messages during documentation build have been
+   squelched.
+
+Also contains various documentation updates, code clean-ups and minor fixups.
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/Documentation/git-ls-remote.txt b/Documentation/git-ls-remote.txt
index a2ea1fd..0a5c8b7 100644
--- a/Documentation/git-ls-remote.txt
+++ b/Documentation/git-ls-remote.txt
@@ -28,7 +28,9 @@
 	Limit to only refs/heads and refs/tags, respectively.
 	These options are _not_ mutually exclusive; when given
 	both, references stored in refs/heads and refs/tags are
-	displayed.
+	displayed.  Note that `git ls-remote -h` used without
+	anything else on the command line gives help, consistent
+	with other git subcommands.
 
 --refs::
 	Do not show peeled tags or pseudorefs like `HEAD` in the output.
diff --git a/Documentation/gitcli.txt b/Documentation/gitcli.txt
index 373cfa2..92e4ba6 100644
--- a/Documentation/gitcli.txt
+++ b/Documentation/gitcli.txt
@@ -126,6 +126,11 @@
     --long                always use long format
     --abbrev[=<n>]        use <n> digits to display SHA-1s
 ---------------------------------------------
++
+Note that some subcommand (e.g. `git grep`) may behave differently
+when there are things on the command line other than `-h`, but `git
+subcmd -h` without anything else on the command line is meant to
+consistently give the usage.
 
 --help-all::
 	Some Git commands take options that are only used for plumbing or that
diff --git a/GIT-VERSION-GEN b/GIT-VERSION-GEN
index 2b7f62b..2a8e709 100755
--- a/GIT-VERSION-GEN
+++ b/GIT-VERSION-GEN
@@ -1,7 +1,7 @@
 #!/bin/sh
 
 GVF=GIT-VERSION-FILE
-DEF_VER=v2.25.0
+DEF_VER=v2.25.1
 
 LF='
 '
diff --git a/RelNotes b/RelNotes
index 091dd02..c63ee7d 120000
--- a/RelNotes
+++ b/RelNotes
@@ -1 +1 @@
-Documentation/RelNotes/2.25.0.txt
\ No newline at end of file
+Documentation/RelNotes/2.25.1.txt
\ No newline at end of file
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/fetch.c b/builtin/fetch.c
index b4c6d92..fd69c4f 100644
--- a/builtin/fetch.c
+++ b/builtin/fetch.c
@@ -335,6 +335,7 @@
 	struct string_list_item *remote_ref_item;
 	const struct ref *ref;
 	struct refname_hash_entry *item = NULL;
+	const int quick_flags = OBJECT_INFO_QUICK | OBJECT_INFO_SKIP_FETCH_OBJECT;
 
 	refname_hash_init(&existing_refs);
 	refname_hash_init(&remote_refs);
@@ -353,10 +354,9 @@
 		 */
 		if (ends_with(ref->name, "^{}")) {
 			if (item &&
-			    !has_object_file_with_flags(&ref->old_oid,
-							OBJECT_INFO_QUICK) &&
+			    !has_object_file_with_flags(&ref->old_oid, quick_flags) &&
 			    !oidset_contains(&fetch_oids, &ref->old_oid) &&
-			    !has_object_file_with_flags(&item->oid, OBJECT_INFO_QUICK) &&
+			    !has_object_file_with_flags(&item->oid, quick_flags) &&
 			    !oidset_contains(&fetch_oids, &item->oid))
 				clear_item(item);
 			item = NULL;
@@ -370,7 +370,7 @@
 		 * fetch.
 		 */
 		if (item &&
-		    !has_object_file_with_flags(&item->oid, OBJECT_INFO_QUICK) &&
+		    !has_object_file_with_flags(&item->oid, quick_flags) &&
 		    !oidset_contains(&fetch_oids, &item->oid))
 			clear_item(item);
 
@@ -391,7 +391,7 @@
 	 * checked to see if it needs fetching.
 	 */
 	if (item &&
-	    !has_object_file_with_flags(&item->oid, OBJECT_INFO_QUICK) &&
+	    !has_object_file_with_flags(&item->oid, quick_flags) &&
 	    !oidset_contains(&fetch_oids, &item->oid))
 		clear_item(item);
 
diff --git a/builtin/fmt-merge-msg.c b/builtin/fmt-merge-msg.c
index 05a92c5..736f666 100644
--- a/builtin/fmt-merge-msg.c
+++ b/builtin/fmt-merge-msg.c
@@ -494,7 +494,6 @@
 		enum object_type type;
 		unsigned long size, len;
 		char *buf = read_object_file(oid, &type, &size);
-		struct signature_check sigc = { 0 };
 		struct strbuf sig = STRBUF_INIT;
 
 		if (!buf || type != OBJ_TAG)
@@ -503,12 +502,10 @@
 
 		if (size == len)
 			; /* merely annotated */
-		else if (!check_signature(buf, len, buf + len, size - len,
-					  &sigc)) {
-			strbuf_addstr(&sig, sigc.gpg_output);
-			signature_check_clear(&sigc);
-		} else
-			strbuf_addstr(&sig, "gpg verification failed.\n");
+		else if (verify_signed_buffer(buf, len, buf + len, size - len, &sig, NULL)) {
+			if (!sig.len)
+				strbuf_addstr(&sig, "gpg verification failed.\n");
+		}
 
 		if (!tag_number++) {
 			fmt_tag_signature(&tagbuf, &sig, buf, len);
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/mingw.c b/compat/mingw.c
index 402c1ad..b523014 100644
--- a/compat/mingw.c
+++ b/compat/mingw.c
@@ -13,6 +13,19 @@
 
 static const int delay[] = { 0, 1, 10, 20, 40 };
 
+void open_in_gdb(void)
+{
+	static struct child_process cp = CHILD_PROCESS_INIT;
+	extern char *_pgmptr;
+
+	argv_array_pushl(&cp.args, "mintty", "gdb", NULL);
+	argv_array_pushf(&cp.args, "--pid=%d", getpid());
+	cp.clean_on_exit = 1;
+	if (start_command(&cp) < 0)
+		die_errno("Could not start gdb");
+	sleep(1);
+}
+
 int err_win_to_posix(DWORD winerr)
 {
 	int error = ENOSYS;
diff --git a/compat/mingw.h b/compat/mingw.h
index 714bc1d..e6fe810 100644
--- a/compat/mingw.h
+++ b/compat/mingw.h
@@ -599,6 +599,16 @@
 int main(int argc, const char **argv);
 
 /*
+ * For debugging: if a problem occurs, say, in a Git process that is spawned
+ * from another Git process which in turn is spawned from yet another Git
+ * process, it can be quite daunting to figure out what is going on.
+ *
+ * Call this function to open a new MinTTY (this assumes you are in Git for
+ * Windows' SDK) with a GDB that attaches to the current process right away.
+ */
+extern void open_in_gdb(void);
+
+/*
  * Used by Pthread API implementation for Windows
  */
 int err_win_to_posix(DWORD winerr);
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/compat/poll/poll.c b/compat/poll/poll.c
index 0e95dd4..afa6d24 100644
--- a/compat/poll/poll.c
+++ b/compat/poll/poll.c
@@ -139,22 +139,10 @@
   INPUT_RECORD *irbuffer;
   DWORD avail, nbuffer;
   BOOL bRet;
-  IO_STATUS_BLOCK iosb;
-  FILE_PIPE_LOCAL_INFORMATION fpli;
-  static PNtQueryInformationFile NtQueryInformationFile;
-  static BOOL once_only;
 
   switch (GetFileType (h))
     {
     case FILE_TYPE_PIPE:
-      if (!once_only)
-	{
-	  NtQueryInformationFile = (PNtQueryInformationFile)(void (*)(void))
-	    GetProcAddress (GetModuleHandleW (L"ntdll.dll"),
-			    "NtQueryInformationFile");
-	  once_only = TRUE;
-	}
-
       happened = 0;
       if (PeekNamedPipe (h, NULL, 0, NULL, &avail, NULL) != 0)
 	{
@@ -166,22 +154,9 @@
 
       else
 	{
-	  /* It was the write-end of the pipe.  Check if it is writable.
-	     If NtQueryInformationFile fails, optimistically assume the pipe is
-	     writable.  This could happen on Win9x, where NtQueryInformationFile
-	     is not available, or if we inherit a pipe that doesn't permit
-	     FILE_READ_ATTRIBUTES access on the write end (I think this should
-	     not happen since WinXP SP2; WINE seems fine too).  Otherwise,
-	     ensure that enough space is available for atomic writes.  */
-	  memset (&iosb, 0, sizeof (iosb));
-	  memset (&fpli, 0, sizeof (fpli));
-
-	  if (!NtQueryInformationFile
-	      || NtQueryInformationFile (h, &iosb, &fpli, sizeof (fpli),
-					 FilePipeLocalInformation)
-	      || fpli.WriteQuotaAvailable >= PIPE_BUF
-	      || (fpli.OutboundQuota < PIPE_BUF &&
-		  fpli.WriteQuotaAvailable == fpli.OutboundQuota))
+	  /* It was the write-end of the pipe. Unfortunately there is no
+	     reliable way of knowing if it can be written without blocking.
+	     Just say that it's all good. */
 	    happened |= *p_sought & (POLLOUT | POLLWRNORM | POLLWRBAND);
 	}
       return happened;
diff --git a/gpg-interface.c b/gpg-interface.c
index 5134ce2..131e7d5 100644
--- a/gpg-interface.c
+++ b/gpg-interface.c
@@ -207,55 +207,6 @@
 	FREE_AND_NULL(sigc->key);
 }
 
-static int verify_signed_buffer(const char *payload, size_t payload_size,
-				const char *signature, size_t signature_size,
-				struct strbuf *gpg_output,
-				struct strbuf *gpg_status)
-{
-	struct child_process gpg = CHILD_PROCESS_INIT;
-	struct gpg_format *fmt;
-	struct tempfile *temp;
-	int ret;
-	struct strbuf buf = STRBUF_INIT;
-
-	temp = mks_tempfile_t(".git_vtag_tmpXXXXXX");
-	if (!temp)
-		return error_errno(_("could not create temporary file"));
-	if (write_in_full(temp->fd, signature, signature_size) < 0 ||
-	    close_tempfile_gently(temp) < 0) {
-		error_errno(_("failed writing detached signature to '%s'"),
-			    temp->filename.buf);
-		delete_tempfile(&temp);
-		return -1;
-	}
-
-	fmt = get_format_by_sig(signature);
-	if (!fmt)
-		BUG("bad signature '%s'", signature);
-
-	argv_array_push(&gpg.args, fmt->program);
-	argv_array_pushv(&gpg.args, fmt->verify_args);
-	argv_array_pushl(&gpg.args,
-			 "--status-fd=1",
-			 "--verify", temp->filename.buf, "-",
-			 NULL);
-
-	if (!gpg_status)
-		gpg_status = &buf;
-
-	sigchain_push(SIGPIPE, SIG_IGN);
-	ret = pipe_command(&gpg, payload, payload_size,
-			   gpg_status, 0, gpg_output, 0);
-	sigchain_pop(SIGPIPE);
-
-	delete_tempfile(&temp);
-
-	ret |= !strstr(gpg_status->buf, "\n[GNUPG:] GOODSIG ");
-	strbuf_release(&buf); /* no matter it was used or not */
-
-	return ret;
-}
-
 int check_signature(const char *payload, size_t plen, const char *signature,
 	size_t slen, struct signature_check *sigc)
 {
@@ -400,3 +351,51 @@
 
 	return 0;
 }
+
+int verify_signed_buffer(const char *payload, size_t payload_size,
+			 const char *signature, size_t signature_size,
+			 struct strbuf *gpg_output, struct strbuf *gpg_status)
+{
+	struct child_process gpg = CHILD_PROCESS_INIT;
+	struct gpg_format *fmt;
+	struct tempfile *temp;
+	int ret;
+	struct strbuf buf = STRBUF_INIT;
+
+	temp = mks_tempfile_t(".git_vtag_tmpXXXXXX");
+	if (!temp)
+		return error_errno(_("could not create temporary file"));
+	if (write_in_full(temp->fd, signature, signature_size) < 0 ||
+	    close_tempfile_gently(temp) < 0) {
+		error_errno(_("failed writing detached signature to '%s'"),
+			    temp->filename.buf);
+		delete_tempfile(&temp);
+		return -1;
+	}
+
+	fmt = get_format_by_sig(signature);
+	if (!fmt)
+		BUG("bad signature '%s'", signature);
+
+	argv_array_push(&gpg.args, fmt->program);
+	argv_array_pushv(&gpg.args, fmt->verify_args);
+	argv_array_pushl(&gpg.args,
+			 "--status-fd=1",
+			 "--verify", temp->filename.buf, "-",
+			 NULL);
+
+	if (!gpg_status)
+		gpg_status = &buf;
+
+	sigchain_push(SIGPIPE, SIG_IGN);
+	ret = pipe_command(&gpg, payload, payload_size,
+			   gpg_status, 0, gpg_output, 0);
+	sigchain_pop(SIGPIPE);
+
+	delete_tempfile(&temp);
+
+	ret |= !strstr(gpg_status->buf, "\n[GNUPG:] GOODSIG ");
+	strbuf_release(&buf); /* no matter it was used or not */
+
+	return ret;
+}
diff --git a/gpg-interface.h b/gpg-interface.h
index 93cc3af..3e624ec 100644
--- a/gpg-interface.h
+++ b/gpg-interface.h
@@ -46,6 +46,15 @@
 int sign_buffer(struct strbuf *buffer, struct strbuf *signature,
 		const char *signing_key);
 
+/*
+ * Run "gpg" to see if the payload matches the detached signature.
+ * gpg_output, when set, receives the diagnostic output from GPG.
+ * gpg_status, when set, receives the status output from GPG.
+ */
+int verify_signed_buffer(const char *payload, size_t payload_size,
+			 const char *signature, size_t signature_size,
+			 struct strbuf *gpg_output, struct strbuf *gpg_status);
+
 int git_gpg_config(const char *, const char *, void *);
 void set_signing_key(const char *);
 const char *get_signing_key(void);
diff --git a/log-tree.c b/log-tree.c
index 4e32638..32d17c9 100644
--- a/log-tree.c
+++ b/log-tree.c
@@ -449,22 +449,22 @@
 {
 	struct strbuf payload = STRBUF_INIT;
 	struct strbuf signature = STRBUF_INIT;
-	struct signature_check sigc = { 0 };
+	struct strbuf gpg_output = STRBUF_INIT;
 	int status;
 
 	if (parse_signed_commit(commit, &payload, &signature) <= 0)
 		goto out;
 
-	status = check_signature(payload.buf, payload.len, signature.buf,
-				 signature.len, &sigc);
-	if (status && sigc.result == 'N')
-		show_sig_lines(opt, status, "No signature\n");
-	else {
-		show_sig_lines(opt, status, sigc.gpg_output);
-		signature_check_clear(&sigc);
-	}
+	status = verify_signed_buffer(payload.buf, payload.len,
+				      signature.buf, signature.len,
+				      &gpg_output, NULL);
+	if (status && !gpg_output.len)
+		strbuf_addstr(&gpg_output, "No signature\n");
+
+	show_sig_lines(opt, status, gpg_output.buf);
 
  out:
+	strbuf_release(&gpg_output);
 	strbuf_release(&payload);
 	strbuf_release(&signature);
 }
@@ -497,7 +497,6 @@
 	struct object_id oid;
 	struct tag *tag;
 	struct strbuf verify_message;
-	struct signature_check sigc = { 0 };
 	int status, nth;
 	size_t payload_size, gpg_message_offset;
 
@@ -516,7 +515,7 @@
 			    "merged tag '%s'\n", tag->tag);
 	else if ((nth = which_parent(&tag->tagged->oid, commit)) < 0)
 		strbuf_addf(&verify_message, "tag %s names a non-parent %s\n",
-				    tag->tag, tag->tagged->oid.hash);
+				    tag->tag, oid_to_hex(&tag->tagged->oid));
 	else
 		strbuf_addf(&verify_message,
 			    "parent #%d, tagged '%s'\n", nth + 1, tag->tag);
@@ -526,13 +525,12 @@
 	status = -1;
 	if (extra->len > payload_size) {
 		/* could have a good signature */
-		if (!check_signature(extra->value, payload_size,
-				     extra->value + payload_size,
-				     extra->len - payload_size, &sigc)) {
-			strbuf_addstr(&verify_message, sigc.gpg_output);
-			signature_check_clear(&sigc);
+		if (!verify_signed_buffer(extra->value, payload_size,
+					  extra->value + payload_size,
+					  extra->len - payload_size,
+					  &verify_message, NULL))
 			status = 0; /* good */
-		} else if (verify_message.len <= gpg_message_offset)
+		else if (verify_message.len <= gpg_message_offset)
 			strbuf_addstr(&verify_message, "No signature\n");
 		/* otherwise we couldn't verify, which is shown as bad */
 	}
diff --git a/merge-recursive.c b/merge-recursive.c
index 10dca56..e6f943c 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -998,10 +998,13 @@
 		free(buf);
 	}
 update_index:
-	if (!ret && update_cache)
-		if (add_cacheinfo(opt, contents, path, 0, update_wd,
+	if (!ret && update_cache) {
+		int refresh = (!opt->priv->call_depth &&
+			       contents->mode != S_IFGITLINK);
+		if (add_cacheinfo(opt, contents, path, 0, refresh,
 				  ADD_CACHE_OK_TO_ADD))
 			return -1;
+	}
 	return ret;
 }
 
@@ -1712,6 +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)
 {
@@ -1756,14 +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;
@@ -1776,7 +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,
@@ -1797,7 +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,
@@ -1846,7 +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/t3433-rebase-across-mode-change.sh b/t/t3433-rebase-across-mode-change.sh
new file mode 100755
index 0000000..05df964
--- /dev/null
+++ b/t/t3433-rebase-across-mode-change.sh
@@ -0,0 +1,48 @@
+#!/bin/sh
+
+test_description='git rebase across mode change'
+
+. ./test-lib.sh
+
+test_expect_success 'setup' '
+	mkdir DS &&
+	>DS/whatever &&
+	git add DS &&
+	git commit -m base &&
+
+	git branch side1 &&
+	git branch side2 &&
+
+	git checkout side1 &&
+	git rm -rf DS &&
+	test_ln_s_add unrelated DS &&
+	git commit -m side1 &&
+
+	git checkout side2 &&
+	>unrelated &&
+	git add unrelated &&
+	git commit -m commit1 &&
+
+	echo >>unrelated &&
+	git commit -am commit2
+'
+
+test_expect_success 'rebase changes with the apply backend' '
+	test_when_finished "git rebase --abort || true" &&
+	git checkout -b apply-backend side2 &&
+	git rebase side1
+'
+
+test_expect_success 'rebase changes with the merge backend' '
+	test_when_finished "git rebase --abort || true" &&
+	git checkout -b merge-backend side2 &&
+	git rebase -m side1
+'
+
+test_expect_success 'rebase changes with the merge backend with a delay' '
+	test_when_finished "git rebase --abort || true" &&
+	git checkout -b merge-delay-backend side2 &&
+	git rebase -m --exec "sleep 1" side1
+'
+
+test_done
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/t4202-log.sh b/t/t4202-log.sh
index 2c94894..c9c10ca 100755
--- a/t/t4202-log.sh
+++ b/t/t4202-log.sh
@@ -1631,6 +1631,26 @@
 	grep "^| | gpg: Good signature" actual
 '
 
+test_expect_success GPG 'log --graph --show-signature for merged tag in shallow clone' '
+	test_when_finished "git reset --hard && git checkout master" &&
+	git checkout -b plain-shallow master &&
+	echo aaa >bar &&
+	git add bar &&
+	git commit -m bar_commit &&
+	git checkout --detach master &&
+	echo bbb >baz &&
+	git add baz &&
+	git commit -m baz_commit &&
+	git tag -s -m signed_tag_msg signed_tag_shallow &&
+	hash=$(git rev-parse HEAD) &&
+	git checkout plain-shallow &&
+	git merge --no-ff -m msg signed_tag_shallow &&
+	git clone --depth 1 --no-local . shallow &&
+	test_when_finished "rm -rf shallow" &&
+	git -C shallow log --graph --show-signature -n1 plain-shallow >actual &&
+	grep "tag signed_tag_shallow names a non-parent $hash" actual
+'
+
 test_expect_success GPGSM 'log --graph --show-signature for merged tag x509' '
 	test_when_finished "git reset --hard && git checkout master" &&
 	test_config gpg.format x509 &&
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/t5580-clone-push-unc.sh b/t/t5580-unc-paths.sh
similarity index 89%
rename from t/t5580-clone-push-unc.sh
rename to t/t5580-unc-paths.sh
index 01b52c1..cf768b3 100755
--- a/t/t5580-clone-push-unc.sh
+++ b/t/t5580-unc-paths.sh
@@ -40,11 +40,23 @@
 	git clone "file://$UNCPATH" clone
 '
 
+test_expect_success 'clone without file://' '
+	git clone "$UNCPATH" clone-without-file
+'
+
 test_expect_success 'clone with backslashed path' '
 	BACKSLASHED="$(echo "$UNCPATH" | tr / \\\\)" &&
 	git clone "$BACKSLASHED" backslashed
 '
 
+test_expect_success fetch '
+	git init to-fetch &&
+	(
+		cd to-fetch &&
+		git fetch "$UNCPATH" master
+	)
+'
+
 test_expect_success push '
 	(
 		cd clone &&
diff --git a/t/t5616-partial-clone.sh b/t/t5616-partial-clone.sh
index 9a9178f..3988a9c 100755
--- a/t/t5616-partial-clone.sh
+++ b/t/t5616-partial-clone.sh
@@ -384,6 +384,37 @@
 	grep "want $(cat hash)" trace
 '
 
+# The following two tests must be in this order, or else
+# the first will not fail. It is important that the srv.bare
+# repository did not have tags during clone, but has tags
+# in the fetch.
+
+test_expect_failure 'verify fetch succeeds when asking for new tags' '
+	git clone --filter=blob:none "file://$(pwd)/srv.bare" tag-test &&
+	for i in I J K
+	do
+		test_commit -C src $i &&
+		git -C src branch $i || return 1
+	done &&
+	git -C srv.bare fetch --tags origin +refs/heads/*:refs/heads/* &&
+	git -C tag-test -c protocol.version=2 fetch --tags origin
+'
+
+test_expect_success 'verify fetch downloads only one pack when updating refs' '
+	git clone --filter=blob:none "file://$(pwd)/srv.bare" pack-test &&
+	ls pack-test/.git/objects/pack/*pack >pack-list &&
+	test_line_count = 2 pack-list &&
+	for i in A B C
+	do
+		test_commit -C src $i &&
+		git -C src branch $i || return 1
+	done &&
+	git -C srv.bare fetch origin +refs/heads/*:refs/heads/* &&
+	git -C pack-test fetch origin &&
+	ls pack-test/.git/objects/pack/*pack >pack-list &&
+	test_line_count = 3 pack-list
+'
+
 . "$TEST_DIRECTORY"/lib-httpd.sh
 start_httpd
 
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/t/test-lib.sh b/t/test-lib.sh
index 44df51b..0ea1e5a 100644
--- a/t/test-lib.sh
+++ b/t/test-lib.sh
@@ -1083,7 +1083,8 @@
 
 		# adjust the overall time
 		junit_time=$(test-tool date getnanos $junit_suite_start)
-		sed "s/<testsuite [^>]*/& time=\"$junit_time\"/" \
+		sed -e "s/\(<testsuite.*\) time=\"[^\"]*\"/\1/" \
+			-e "s/<testsuite [^>]*/& time=\"$junit_time\"/" \
 			<"$junit_xml_path" >"$junit_xml_path.new"
 		mv "$junit_xml_path.new" "$junit_xml_path"
 
diff --git a/unpack-trees.c b/unpack-trees.c
index 191e738..da4d6d4 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -372,15 +372,20 @@
 	state.refresh_cache = 1;
 	state.istate = index;
 
+	if (!o->update || o->dry_run) {
+		remove_marked_cache_entries(index, 0);
+		trace_performance_leave("check_updates");
+		return 0;
+	}
+
 	if (o->clone)
 		setup_collided_checkout_detection(&state, index);
 
 	progress = get_progress(o);
 
-	if (o->update)
-		git_attr_set_direction(GIT_ATTR_CHECKOUT);
+	git_attr_set_direction(GIT_ATTR_CHECKOUT);
 
-	if (should_update_submodules() && o->update && !o->dry_run)
+	if (should_update_submodules())
 		load_gitmodules_file(index, NULL);
 
 	for (i = 0; i < index->cache_nr; i++) {
@@ -388,18 +393,18 @@
 
 		if (ce->ce_flags & CE_WT_REMOVE) {
 			display_progress(progress, ++cnt);
-			if (o->update && !o->dry_run)
-				unlink_entry(ce);
+			unlink_entry(ce);
 		}
 	}
+
 	remove_marked_cache_entries(index, 0);
 	remove_scheduled_dirs();
 
-	if (should_update_submodules() && o->update && !o->dry_run)
+	if (should_update_submodules())
 		load_gitmodules_file(index, &state);
 
 	enable_delayed_checkout(&state);
-	if (has_promisor_remote() && o->update && !o->dry_run) {
+	if (has_promisor_remote()) {
 		/*
 		 * Prefetch the objects that are to be checked out in the loop
 		 * below.
@@ -431,15 +436,12 @@
 				    ce->name);
 			display_progress(progress, ++cnt);
 			ce->ce_flags &= ~CE_UPDATE;
-			if (o->update && !o->dry_run) {
-				errs |= checkout_entry(ce, &state, NULL, NULL);
-			}
+			errs |= checkout_entry(ce, &state, NULL, NULL);
 		}
 	}
 	stop_progress(&progress);
 	errs |= finish_delayed_checkout(&state, NULL);
-	if (o->update)
-		git_attr_set_direction(GIT_ATTR_CHECKIN);
+	git_attr_set_direction(GIT_ATTR_CHECKIN);
 
 	if (o->clone)
 		report_collided_checkout(index);
@@ -1350,7 +1352,7 @@
 			    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;
 	}
 }