15 files changed, 283 insertions, 159 deletions
diff --git a/builtin/branch.c b/builtin/branch.c
index 52688f2e1b..0552c42ad1 100644
--- a/builtin/branch.c
+++ b/builtin/branch.c
@@ -562,7 +562,9 @@ int cmd_branch(int argc, const char **argv, const char *prefix)
 		OPT_SET_INT('r', "remotes",     &filter.kind, N_("act on remote-tracking branches"),
 			FILTER_REFS_REMOTES),
 		OPT_CONTAINS(&filter.with_commit, N_("print only branches that contain the commit")),
+		OPT_NO_CONTAINS(&filter.no_commit, N_("print only branches that don't contain the commit")),
 		OPT_WITH(&filter.with_commit, N_("print only branches that contain the commit")),
+		OPT_WITHOUT(&filter.no_commit, N_("print only branches that don't contain the commit")),
 		OPT__ABBREV(&filter.abbrev),
 
 		OPT_GROUP(N_("Specific git-branch actions:")),
@@ -618,7 +620,8 @@ int cmd_branch(int argc, const char **argv, const char *prefix)
 	if (!delete && !rename && !edit_description && !new_upstream && !unset_upstream && argc == 0)
 		list = 1;
 
-	if (filter.with_commit || filter.merge != REF_FILTER_MERGED_NONE || filter.points_at.nr)
+	if (filter.with_commit || filter.merge != REF_FILTER_MERGED_NONE || filter.points_at.nr ||
+	    filter.no_commit)
 		list = 1;
 
 	if (!!delete + !!rename + !!new_upstream +
diff --git a/builtin/checkout.c b/builtin/checkout.c
index 81f07c3ef2..3ecc47bec0 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -21,12 +21,31 @@
 #include "submodule-config.h"
 #include "submodule.h"
 
+static int recurse_submodules = RECURSE_SUBMODULES_DEFAULT;
+
 static const char * const checkout_usage[] = {
 	N_("git checkout [<options>] <branch>"),
 	N_("git checkout [<options>] [<branch>] -- <file>..."),
 	NULL,
 };
 
+static int option_parse_recurse_submodules(const struct option *opt,
+					   const char *arg, int unset)
+{
+	if (unset) {
+		recurse_submodules = RECURSE_SUBMODULES_OFF;
+		return 0;
+	}
+	if (arg)
+		recurse_submodules =
+			parse_update_recurse_submodules_arg(opt->long_name,
+							    arg);
+	else
+		recurse_submodules = RECURSE_SUBMODULES_ON;
+
+	return 0;
+}
+
 struct checkout_opts {
 	int patch_mode;
 	int quiet;
@@ -1163,6 +1182,9 @@ int cmd_checkout(int argc, const char **argv, const char *prefix)
 				N_("second guess 'git checkout <no-such-branch>'")),
 		OPT_BOOL(0, "ignore-other-worktrees", &opts.ignore_other_worktrees,
 			 N_("do not check if another worktree is holding the given ref")),
+		{ OPTION_CALLBACK, 0, "recurse-submodules", &recurse_submodules,
+			    "checkout", "control recursive updating of submodules",
+			    PARSE_OPT_OPTARG, option_parse_recurse_submodules },
 		OPT_BOOL(0, "progress", &opts.show_progress, N_("force progress reporting")),
 		OPT_END(),
 	};
@@ -1193,6 +1215,12 @@ int cmd_checkout(int argc, const char **argv, const char *prefix)
 		git_xmerge_config("merge.conflictstyle", conflict_style, NULL);
 	}
 
+	if (recurse_submodules != RECURSE_SUBMODULES_OFF) {
+		git_config(submodule_config, NULL);
+		if (recurse_submodules != RECURSE_SUBMODULES_DEFAULT)
+			set_config_update_recurse_submodules(recurse_submodules);
+	}
+
 	if ((!!opts.new_branch + !!opts.new_branch_force + !!opts.new_orphan_branch) > 1)
 		die(_("-b, -B and --orphan are mutually exclusive"));
 
diff --git a/builtin/clone.c b/builtin/clone.c
index b4c929bb8a..de85b85254 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -39,7 +39,7 @@ static const char * const builtin_clone_usage[] = {
 };
 
 static int option_no_checkout, option_bare, option_mirror, option_single_branch = -1;
-static int option_local = -1, option_no_hardlinks, option_shared, option_recursive;
+static int option_local = -1, option_no_hardlinks, option_shared;
 static int option_shallow_submodules;
 static int deepen;
 static char *option_template, *option_depth, *option_since;
@@ -56,6 +56,21 @@ static struct string_list option_required_reference = STRING_LIST_INIT_NODUP;
 static struct string_list option_optional_reference = STRING_LIST_INIT_NODUP;
 static int option_dissociate;
 static int max_jobs = -1;
+static struct string_list option_recurse_submodules = STRING_LIST_INIT_NODUP;
+
+static int recurse_submodules_cb(const struct option *opt,
+				 const char *arg, int unset)
+{
+	if (unset)
+		string_list_clear((struct string_list *)opt->value, 0);
+	else if (arg)
+		string_list_append((struct string_list *)opt->value, arg);
+	else
+		string_list_append((struct string_list *)opt->value,
+				   (const char *)opt->defval);
+
+	return 0;
+}
 
 static struct option builtin_clone_options[] = {
 	OPT__VERBOSITY(&option_verbosity),
@@ -74,10 +89,13 @@ static struct option builtin_clone_options[] = {
 		    N_("don't use local hardlinks, always copy")),
 	OPT_BOOL('s', "shared", &option_shared,
 		    N_("setup as shared repository")),
-	OPT_BOOL(0, "recursive", &option_recursive,
-		    N_("initialize submodules in the clone")),
-	OPT_BOOL(0, "recurse-submodules", &option_recursive,
-		    N_("initialize submodules in the clone")),
+	{ OPTION_CALLBACK, 0, "recursive", &option_recurse_submodules,
+	  N_("pathspec"), N_("initialize submodules in the clone"),
+	  PARSE_OPT_OPTARG | PARSE_OPT_HIDDEN, recurse_submodules_cb,
+	  (intptr_t)"." },
+	{ OPTION_CALLBACK, 0, "recurse-submodules", &option_recurse_submodules,
+	  N_("pathspec"), N_("initialize submodules in the clone"),
+	  PARSE_OPT_OPTARG, recurse_submodules_cb, (intptr_t)"." },
 	OPT_INTEGER('j', "jobs", &max_jobs,
 		    N_("number of submodules cloned in parallel")),
 	OPT_STRING(0, "template", &option_template, N_("template-directory"),
@@ -733,7 +751,7 @@ static int checkout(int submodule_progress)
 	err |= run_hook_le(NULL, "post-checkout", sha1_to_hex(null_sha1),
 			   oid_to_hex(&oid), "1", NULL);
 
-	if (!err && option_recursive) {
+	if (!err && (option_recurse_submodules.nr > 0)) {
 		struct argv_array args = ARGV_ARRAY_INIT;
 		argv_array_pushl(&args, "submodule", "update", "--init", "--recursive", NULL);
 
@@ -957,7 +975,25 @@ int cmd_clone(int argc, const char **argv, const char *prefix)
 			fprintf(stderr, _("Cloning into '%s'...\n"), dir);
 	}
 
-	if (option_recursive) {
+	if (option_recurse_submodules.nr > 0) {
+		struct string_list_item *item;
+		struct strbuf sb = STRBUF_INIT;
+
+		/* remove duplicates */
+		string_list_sort(&option_recurse_submodules);
+		string_list_remove_duplicates(&option_recurse_submodules, 0);
+
+		/*
+		 * NEEDSWORK: In a multi-working-tree world, this needs to be
+		 * set in the per-worktree config.
+		 */
+		for_each_string_list_item(item, &option_recurse_submodules) {
+			strbuf_addf(&sb, "submodule.active=%s",
+				    item->string);
+			string_list_append(&option_config,
+					   strbuf_detach(&sb, NULL));
+		}
+
 		if (option_required_reference.nr &&
 		    option_optional_reference.nr)
 			die(_("clone --recursive is not compatible with "
diff --git a/builtin/describe.c b/builtin/describe.c
index 45adbf67d5..a5cd8c513f 100644
--- a/builtin/describe.c
+++ b/builtin/describe.c
@@ -50,7 +50,7 @@ struct commit_name {
 };
 
 static const char *prio_names[] = {
-	"head", "lightweight", "annotated",
+	N_("head"), N_("lightweight"), N_("annotated"),
 };
 
 static int commit_name_cmp(const struct commit_name *cn1,
@@ -395,10 +395,19 @@ static void describe(const char *arg, int last_one)
 	free_commit_list(list);
 
 	if (debug) {
+		static int label_width = -1;
+		if (label_width < 0) {
+			int i, w;
+			for (i = 0; i < ARRAY_SIZE(prio_names); i++) {
+				w = strlen(_(prio_names[i]));
+				if (label_width < w)
+					label_width = w;
+			}
+		}
 		for (cur_match = 0; cur_match < match_cnt; cur_match++) {
 			struct possible_tag *t = &all_matches[cur_match];
-			fprintf(stderr, " %-11s %8d %s\n",
-				prio_names[t->name->prio],
+			fprintf(stderr, " %-*s %8d %s\n",
+				label_width, _(prio_names[t->name->prio]),
 				t->depth, t->name->path);
 		}
 		fprintf(stderr, _("traversed %lu commits\n"), seen_commits);
diff --git a/builtin/for-each-ref.c b/builtin/for-each-ref.c
index df41fa0350..eca365bf89 100644
--- a/builtin/for-each-ref.c
+++ b/builtin/for-each-ref.c
@@ -8,8 +8,8 @@
 static char const * const for_each_ref_usage[] = {
 	N_("git for-each-ref [<options>] [<pattern>]"),
 	N_("git for-each-ref [--points-at <object>]"),
-	N_("git for-each-ref [(--merged | --no-merged) [<object>]]"),
-	N_("git for-each-ref [--contains [<object>]]"),
+	N_("git for-each-ref [(--merged | --no-merged) [<commit>]]"),
+	N_("git for-each-ref [--contains [<commit>]] [--no-contains [<commit>]]"),
 	NULL
 };
 
@@ -43,6 +43,7 @@ int cmd_for_each_ref(int argc, const char **argv, const char *prefix)
 		OPT_MERGED(&filter, N_("print only refs that are merged")),
 		OPT_NO_MERGED(&filter, N_("print only refs that are not merged")),
 		OPT_CONTAINS(&filter.with_commit, N_("print only refs which contain the commit")),
+		OPT_NO_CONTAINS(&filter.no_commit, N_("print only refs which don't contain the commit")),
 		OPT_BOOL(0, "ignore-case", &icase, N_("sorting and filtering are case insensitive")),
 		OPT_END(),
 	};
diff --git a/builtin/grep.c b/builtin/grep.c
index 837836fb3e..65070c52fc 100644
--- a/builtin/grep.c
+++ b/builtin/grep.c
@@ -310,10 +310,7 @@ static int grep_oid(struct grep_opt *opt, const struct object_id *oid,
 {
 	struct strbuf pathbuf = STRBUF_INIT;
 
-	if (opt->relative && opt->prefix_length) {
-		quote_path_relative(filename + tree_name_len, opt->prefix, &pathbuf);
-		strbuf_insert(&pathbuf, 0, filename, tree_name_len);
-	} else if (super_prefix) {
+	if (super_prefix) {
 		strbuf_add(&pathbuf, filename, tree_name_len);
 		strbuf_addstr(&pathbuf, super_prefix);
 		strbuf_addstr(&pathbuf, filename + tree_name_len);
@@ -321,6 +318,13 @@ static int grep_oid(struct grep_opt *opt, const struct object_id *oid,
 		strbuf_addstr(&pathbuf, filename);
 	}
 
+	if (opt->relative && opt->prefix_length) {
+		char *name = strbuf_detach(&pathbuf, NULL);
+		quote_path_relative(name + tree_name_len, opt->prefix, &pathbuf);
+		strbuf_insert(&pathbuf, 0, name, tree_name_len);
+		free(name);
+	}
+
 #ifndef NO_PTHREADS
 	if (num_threads) {
 		add_work(opt, GREP_SOURCE_SHA1, pathbuf.buf, path, oid);
@@ -345,12 +349,14 @@ static int grep_file(struct grep_opt *opt, const char *filename)
 {
 	struct strbuf buf = STRBUF_INIT;
 
+	if (super_prefix)
+		strbuf_addstr(&buf, super_prefix);
+	strbuf_addstr(&buf, filename);
+
 	if (opt->relative && opt->prefix_length) {
-		quote_path_relative(filename, opt->prefix, &buf);
-	} else {
-		if (super_prefix)
-			strbuf_addstr(&buf, super_prefix);
-		strbuf_addstr(&buf, filename);
+		char *name = strbuf_detach(&buf, NULL);
+		quote_path_relative(name, opt->prefix, &buf);
+		free(name);
 	}
 
 #ifndef NO_PTHREADS
@@ -399,13 +405,12 @@ static void run_pager(struct grep_opt *opt, const char *prefix)
 }
 
 static void compile_submodule_options(const struct grep_opt *opt,
-				      const struct pathspec *pathspec,
+				      const char **argv,
 				      int cached, int untracked,
 				      int opt_exclude, int use_index,
 				      int pattern_type_arg)
 {
 	struct grep_pat *pattern;
-	int i;
 
 	if (recurse_submodules)
 		argv_array_push(&submodule_options, "--recurse-submodules");
@@ -523,9 +528,8 @@ static void compile_submodule_options(const struct grep_opt *opt,
 
 	/* Add Pathspecs */
 	argv_array_push(&submodule_options, "--");
-	for (i = 0; i < pathspec->nr; i++)
-		argv_array_push(&submodule_options,
-				pathspec->items[i].original);
+	for (; *argv; argv++)
+		argv_array_push(&submodule_options, *argv);
 }
 
 /*
@@ -538,7 +542,7 @@ static int grep_submodule_launch(struct grep_opt *opt,
 	int status, i;
 	const char *end_of_base;
 	const char *name;
-	struct work_item *w = opt->output_priv;
+	struct strbuf child_output = STRBUF_INIT;
 
 	end_of_base = strchr(gs->name, ':');
 	if (gs->identifier && end_of_base)
@@ -549,6 +553,11 @@ static int grep_submodule_launch(struct grep_opt *opt,
 	prepare_submodule_repo_env(&cp.env_array);
 	argv_array_push(&cp.env_array, GIT_DIR_ENVIRONMENT);
 
+	if (opt->relative && opt->prefix_length)
+		argv_array_pushf(&cp.env_array, "%s=%s",
+				 GIT_TOPLEVEL_PREFIX_ENVIRONMENT,
+				 opt->prefix);
+
 	/* Add super prefix */
 	argv_array_pushf(&cp.args, "--super-prefix=%s%s/",
 			 super_prefix ? super_prefix : "",
@@ -593,14 +602,16 @@ static int grep_submodule_launch(struct grep_opt *opt,
 	 * child process.  A '0' indicates a hit, a '1' indicates no hit and
 	 * anything else is an error.
 	 */
-	status = capture_command(&cp, &w->out, 0);
+	status = capture_command(&cp, &child_output, 0);
 	if (status && (status != 1)) {
 		/* flush the buffer */
-		write_or_die(1, w->out.buf, w->out.len);
+		write_or_die(1, child_output.buf, child_output.len);
 		die("process for submodule '%s' failed with exit code: %d",
 		    gs->name, status);
 	}
 
+	opt->output(opt, child_output.buf, child_output.len);
+	strbuf_release(&child_output);
 	/* invert the return code to make a hit equal to 1 */
 	return !status;
 }
@@ -616,7 +627,7 @@ static int grep_submodule(struct grep_opt *opt, const unsigned char *sha1,
 {
 	if (!is_submodule_initialized(path))
 		return 0;
-	if (!is_submodule_populated(path)) {
+	if (!is_submodule_populated_gently(path, NULL)) {
 		/*
 		 * If searching history, check for the presense of the
 		 * submodule's gitdir before skipping the submodule.
@@ -641,19 +652,14 @@ static int grep_submodule(struct grep_opt *opt, const unsigned char *sha1,
 	} else
 #endif
 	{
-		struct work_item w;
+		struct grep_source gs;
 		int hit;
 
-		grep_source_init(&w.source, GREP_SOURCE_SUBMODULE,
+		grep_source_init(&gs, GREP_SOURCE_SUBMODULE,
 				 filename, path, sha1);
-		strbuf_init(&w.out, 0);
-		opt->output_priv = &w;
-		hit = grep_submodule_launch(opt, &w.source);
-
-		write_or_die(1, w.out.buf, w.out.len);
+		hit = grep_submodule_launch(opt, &gs);
 
-		grep_source_clear(&w.source);
-		strbuf_release(&w.out);
+		grep_source_clear(&gs);
 		return hit;
 	}
 }
@@ -979,7 +985,7 @@ int cmd_grep(int argc, const char **argv, const char *prefix)
 		OPT_SET_INT(0, "exclude-standard", &opt_exclude,
 			    N_("ignore files specified via '.gitignore'"), 1),
 		OPT_BOOL(0, "recurse-submodules", &recurse_submodules,
-			 N_("recursivley search in each submodule")),
+			 N_("recursively search in each submodule")),
 		OPT_STRING(0, "parent-basename", &parent_basename,
 			   N_("basename"),
 			   N_("prepend parent project's basename to output")),
@@ -1236,7 +1242,7 @@ int cmd_grep(int argc, const char **argv, const char *prefix)
 
 	if (recurse_submodules) {
 		gitmodules_config();
-		compile_submodule_options(&opt, &pathspec, cached, untracked,
+		compile_submodule_options(&opt, argv + i, cached, untracked,
 					  opt_exclude, use_index,
 					  pattern_type_arg);
 	}
diff --git a/builtin/log.c b/builtin/log.c
index 670229cbb4..b3b10cc1ed 100644
--- a/builtin/log.c
+++ b/builtin/log.c
@@ -52,6 +52,11 @@ struct line_opt_callback_data {
 	struct string_list args;
 };
 
+static int auto_decoration_style(void)
+{
+	return (isatty(1) || pager_in_use()) ? DECORATE_SHORT_REFS : 0;
+}
+
 static int parse_decoration_style(const char *var, const char *value)
 {
 	switch (git_config_maybe_bool(var, value)) {
@@ -67,7 +72,7 @@ static int parse_decoration_style(const char *var, const char *value)
 	else if (!strcmp(value, "short"))
 		return DECORATE_SHORT_REFS;
 	else if (!strcmp(value, "auto"))
-		return (isatty(1) || pager_in_use()) ? DECORATE_SHORT_REFS : 0;
+		return auto_decoration_style();
 	return -1;
 }
 
@@ -405,6 +410,8 @@ static int git_log_config(const char *var, const char *value, void *cb)
 		if (decoration_style < 0)
 			decoration_style = 0; /* maybe warn? */
 		return 0;
+	} else {
+		decoration_style = auto_decoration_style();
 	}
 	if (!strcmp(var, "log.showroot")) {
 		default_show_root = git_config_bool(var, value);
diff --git a/builtin/ls-files.c b/builtin/ls-files.c
index 1c0f057d02..d449e46db5 100644
--- a/builtin/ls-files.c
+++ b/builtin/ls-files.c
@@ -30,7 +30,7 @@ static int line_terminator = '\n';
 static int debug_mode;
 static int show_eol;
 static int recurse_submodules;
-static struct argv_array submodules_options = ARGV_ARRAY_INIT;
+static struct argv_array submodule_options = ARGV_ARRAY_INIT;
 
 static const char *prefix;
 static const char *super_prefix;
@@ -172,20 +172,27 @@ static void show_killed_files(struct dir_struct *dir)
 /*
  * Compile an argv_array with all of the options supported by --recurse_submodules
  */
-static void compile_submodule_options(const struct dir_struct *dir, int show_tag)
+static void compile_submodule_options(const char **argv,
+				      const struct dir_struct *dir,
+				      int show_tag)
 {
 	if (line_terminator == '\0')
-		argv_array_push(&submodules_options, "-z");
+		argv_array_push(&submodule_options, "-z");
 	if (show_tag)
-		argv_array_push(&submodules_options, "-t");
+		argv_array_push(&submodule_options, "-t");
 	if (show_valid_bit)
-		argv_array_push(&submodules_options, "-v");
+		argv_array_push(&submodule_options, "-v");
 	if (show_cached)
-		argv_array_push(&submodules_options, "--cached");
+		argv_array_push(&submodule_options, "--cached");
 	if (show_eol)
-		argv_array_push(&submodules_options, "--eol");
+		argv_array_push(&submodule_options, "--eol");
 	if (debug_mode)
-		argv_array_push(&submodules_options, "--debug");
+		argv_array_push(&submodule_options, "--debug");
+
+	/* Add Pathspecs */
+	argv_array_push(&submodule_options, "--");
+	for (; *argv; argv++)
+		argv_array_push(&submodule_options, *argv);
 }
 
 /**
@@ -195,8 +202,11 @@ static void show_gitlink(const struct cache_entry *ce)
 {
 	struct child_process cp = CHILD_PROCESS_INIT;
 	int status;
-	int i;
 
+	if (prefix_len)
+		argv_array_pushf(&cp.env_array, "%s=%s",
+				 GIT_TOPLEVEL_PREFIX_ENVIRONMENT,
+				 prefix);
 	argv_array_pushf(&cp.args, "--super-prefix=%s%s/",
 			 super_prefix ? super_prefix : "",
 			 ce->name);
@@ -204,16 +214,7 @@ static void show_gitlink(const struct cache_entry *ce)
 	argv_array_push(&cp.args, "--recurse-submodules");
 
 	/* add supported options */
-	argv_array_pushv(&cp.args, submodules_options.argv);
-
-	/*
-	 * Pass in the original pathspec args.  The submodule will be
-	 * responsible for prepending the 'submodule_prefix' prior to comparing
-	 * against the pathspec for matches.
-	 */
-	argv_array_push(&cp.args, "--");
-	for (i = 0; i < pathspec.nr; i++)
-		argv_array_push(&cp.args, pathspec.items[i].original);
+	argv_array_pushv(&cp.args, submodule_options.argv);
 
 	cp.git_cmd = 1;
 	cp.dir = ce->name;
@@ -604,7 +605,7 @@ int cmd_ls_files(int argc, const char **argv, const char *cmd_prefix)
 		setup_work_tree();
 
 	if (recurse_submodules)
-		compile_submodule_options(&dir, show_tag);
+		compile_submodule_options(argv, &dir, show_tag);
 
 	if (recurse_submodules &&
 	    (show_stage || show_deleted || show_others || show_unmerged ||
diff --git a/builtin/merge.c b/builtin/merge.c
index 7554b8d412..95572b1810 100644
--- a/builtin/merge.c
+++ b/builtin/merge.c
@@ -44,7 +44,6 @@ struct strategy {
 
 static const char * const builtin_merge_usage[] = {
 	N_("git merge [<options>] [<commit>...]"),
-	N_("git merge [<options>] <msg> HEAD <commit>"),
 	N_("git merge --abort"),
 	N_("git merge --continue"),
 	NULL
@@ -634,9 +633,10 @@ static void write_tree_trivial(struct object_id *oid)
 
 static int try_merge_strategy(const char *strategy, struct commit_list *common,
 			      struct commit_list *remoteheads,
-			      struct commit *head, const char *head_arg)
+			      struct commit *head)
 {
 	static struct lock_file lock;
+	const char *head_arg = "HEAD";
 
 	hold_locked_index(&lock, LOCK_DIE_ON_ERROR);
 	refresh_cache(REFRESH_QUIET);
@@ -853,24 +853,6 @@ static int suggest_conflicts(void)
 	return 1;
 }
 
-static struct commit *is_old_style_invocation(int argc, const char **argv,
-					      const struct object_id *head)
-{
-	struct commit *second_token = NULL;
-	if (argc > 2) {
-		struct object_id second_oid;
-
-		if (get_oid(argv[1], &second_oid))
-			return NULL;
-		second_token = lookup_commit_reference_gently(second_oid.hash, 0);
-		if (!second_token)
-			die(_("'%s' is not a commit"), argv[1]);
-		if (oidcmp(&second_token->object.oid, head))
-			return NULL;
-	}
-	return second_token;
-}
-
 static int evaluate_result(void)
 {
 	int cnt = 0;
@@ -1120,7 +1102,6 @@ int cmd_merge(int argc, const char **argv, const char *prefix)
 	struct object_id result_tree, stash, head_oid;
 	struct commit *head_commit;
 	struct strbuf buf = STRBUF_INIT;
-	const char *head_arg;
 	int i, ret = 0, head_subsumed;
 	int best_cnt = -1, merge_was_ok = 0, automerge_was_ok = 0;
 	struct commit_list *common = NULL;
@@ -1260,34 +1241,12 @@ int cmd_merge(int argc, const char **argv, const char *prefix)
 	}
 
 	/*
-	 * This could be traditional "merge <msg> HEAD <commit>..."  and
-	 * the way we can tell it is to see if the second token is HEAD,
-	 * but some people might have misused the interface and used a
-	 * commit-ish that is the same as HEAD there instead.
-	 * Traditional format never would have "-m" so it is an
-	 * additional safety measure to check for it.
+	 * All the rest are the commits being merged; prepare
+	 * the standard merge summary message to be appended
+	 * to the given message.
 	 */
-	if (!have_message &&
-	    is_old_style_invocation(argc, argv, &head_commit->object.oid)) {
-		warning("old-style 'git merge <msg> HEAD <commit>' is deprecated.");
-		strbuf_addstr(&merge_msg, argv[0]);
-		head_arg = argv[1];
-		argv += 2;
-		argc -= 2;
-		remoteheads = collect_parents(head_commit, &head_subsumed,
-					      argc, argv, NULL);
-	} else {
-		/* We are invoked directly as the first-class UI. */
-		head_arg = "HEAD";
-
-		/*
-		 * All the rest are the commits being merged; prepare
-		 * the standard merge summary message to be appended
-		 * to the given message.
-		 */
-		remoteheads = collect_parents(head_commit, &head_subsumed,
-					      argc, argv, &merge_msg);
-	}
+	remoteheads = collect_parents(head_commit, &head_subsumed,
+				      argc, argv, &merge_msg);
 
 	if (!head_commit || !argc)
 		usage_with_options(builtin_merge_usage,
@@ -1513,7 +1472,7 @@ int cmd_merge(int argc, const char **argv, const char *prefix)
 
 		ret = try_merge_strategy(use_strategies[i]->name,
 					 common, remoteheads,
-					 head_commit, head_arg);
+					 head_commit);
 		if (!option_commit && !ret) {
 			merge_was_ok = 1;
 			/*
@@ -1583,7 +1542,7 @@ int cmd_merge(int argc, const char **argv, const char *prefix)
 		printf(_("Using the %s to prepare resolving by hand.\n"),
 			best_strategy);
 		try_merge_strategy(best_strategy, common, remoteheads,
-				   head_commit, head_arg);
+				   head_commit);
 	}
 
 	if (squash)
diff --git a/builtin/pack-objects.c b/builtin/pack-objects.c
index 16517f2637..84af7c2324 100644
--- a/builtin/pack-objects.c
+++ b/builtin/pack-objects.c
@@ -239,7 +239,8 @@ static unsigned long write_no_reuse_object(struct sha1file *f, struct object_ent
 					   unsigned long limit, int usable_delta)
 {
 	unsigned long size, datalen;
-	unsigned char header[10], dheader[10];
+	unsigned char header[MAX_PACK_OBJECT_HEADER],
+		      dheader[MAX_PACK_OBJECT_HEADER];
 	unsigned hdrlen;
 	enum object_type type;
 	void *buf;
@@ -286,7 +287,8 @@ static unsigned long write_no_reuse_object(struct sha1file *f, struct object_ent
 	 * The object header is a byte of 'type' followed by zero or
 	 * more bytes of length.
 	 */
-	hdrlen = encode_in_pack_object_header(type, size, header);
+	hdrlen = encode_in_pack_object_header(header, sizeof(header),
+					      type, size);
 
 	if (type == OBJ_OFS_DELTA) {
 		/*
@@ -352,13 +354,15 @@ static off_t write_reuse_object(struct sha1file *f, struct object_entry *entry,
 	off_t offset;
 	enum object_type type = entry->type;
 	off_t datalen;
-	unsigned char header[10], dheader[10];
+	unsigned char header[MAX_PACK_OBJECT_HEADER],
+		      dheader[MAX_PACK_OBJECT_HEADER];
 	unsigned hdrlen;
 
 	if (entry->delta)
 		type = (allow_ofs_delta && entry->delta->idx.offset) ?
 			OBJ_OFS_DELTA : OBJ_REF_DELTA;
-	hdrlen = encode_in_pack_object_header(type, entry->size, header);
+	hdrlen = encode_in_pack_object_header(header, sizeof(header),
+					      type, entry->size);
 
 	offset = entry->in_pack_offset;
 	revidx = find_pack_revindex(p, offset);
diff --git a/builtin/read-tree.c b/builtin/read-tree.c
index 8ba64bc785..23e212ee8c 100644
--- a/builtin/read-tree.c
+++ b/builtin/read-tree.c
@@ -15,10 +15,13 @@
 #include "builtin.h"
 #include "parse-options.h"
 #include "resolve-undo.h"
+#include "submodule.h"
+#include "submodule-config.h"
 
 static int nr_trees;
 static int read_empty;
 static struct tree *trees[MAX_UNPACK_TREES];
+static int recurse_submodules = RECURSE_SUBMODULES_DEFAULT;
 
 static int list_tree(unsigned char *sha1)
 {
@@ -96,6 +99,23 @@ static int debug_merge(const struct cache_entry * const *stages,
 	return 0;
 }
 
+static int option_parse_recurse_submodules(const struct option *opt,
+					   const char *arg, int unset)
+{
+	if (unset) {
+		recurse_submodules = RECURSE_SUBMODULES_OFF;
+		return 0;
+	}
+	if (arg)
+		recurse_submodules =
+			parse_update_recurse_submodules_arg(opt->long_name,
+							    arg);
+	else
+		recurse_submodules = RECURSE_SUBMODULES_ON;
+
+	return 0;
+}
+
 static struct lock_file lock_file;
 
 int cmd_read_tree(int argc, const char **argv, const char *unused_prefix)
@@ -137,6 +157,9 @@ int cmd_read_tree(int argc, const char **argv, const char *unused_prefix)
 			 N_("skip applying sparse checkout filter")),
 		OPT_BOOL(0, "debug-unpack", &opts.debug_unpack,
 			 N_("debug unpack-trees")),
+		{ OPTION_CALLBACK, 0, "recurse-submodules", &recurse_submodules,
+			    "checkout", "control recursive updating of submodules",
+			    PARSE_OPT_OPTARG, option_parse_recurse_submodules },
 		OPT_END()
 	};
 
@@ -152,6 +175,12 @@ int cmd_read_tree(int argc, const char **argv, const char *unused_prefix)
 
 	hold_locked_index(&lock_file, LOCK_DIE_ON_ERROR);
 
+	if (recurse_submodules != RECURSE_SUBMODULES_DEFAULT) {
+		gitmodules_config();
+		git_config(submodule_config, NULL);
+		set_config_update_recurse_submodules(RECURSE_SUBMODULES_ON);
+	}
+
 	prefix_set = opts.prefix ? 1 : 0;
 	if (1 < opts.merge + opts.reset + prefix_set)
 		die("Which one? -m, --reset, or --prefix?");
diff --git a/builtin/receive-pack.c b/builtin/receive-pack.c
index fb2a090a0c..aca9c33d8d 100644
--- a/builtin/receive-pack.c
+++ b/builtin/receive-pack.c
@@ -1524,7 +1524,7 @@ static void queue_commands_from_cert(struct command **tail,
 
 	while (boc < eoc) {
 		const char *eol = memchr(boc, '\n', eoc - boc);
-		tail = queue_command(tail, boc, eol ? eol - boc : eoc - eol);
+		tail = queue_command(tail, boc, eol ? eol - boc : eoc - boc);
 		boc = eol ? eol + 1 : eoc;
 	}
 }
diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index 15a5430c00..85aafe46a4 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -270,6 +270,29 @@ static int module_list_compute(int argc, const char **argv,
 	return result;
 }
 
+static void module_list_active(struct module_list *list)
+{
+	int i;
+	struct module_list active_modules = MODULE_LIST_INIT;
+
+	gitmodules_config();
+
+	for (i = 0; i < list->nr; i++) {
+		const struct cache_entry *ce = list->entries[i];
+
+		if (!is_submodule_initialized(ce->name))
+			continue;
+
+		ALLOC_GROW(active_modules.entries,
+			   active_modules.nr + 1,
+			   active_modules.alloc);
+		active_modules.entries[active_modules.nr++] = ce;
+	}
+
+	free(list->entries);
+	*list = active_modules;
+}
+
 static int module_list(int argc, const char **argv, const char *prefix)
 {
 	int i;
@@ -334,6 +357,18 @@ static void init_submodule(const char *path, const char *prefix, int quiet)
 			displaypath);
 
 	/*
+	 * NEEDSWORK: In a multi-working-tree world, this needs to be
+	 * set in the per-worktree config.
+	 *
+	 * Set active flag for the submodule being initialized
+	 */
+	if (!is_submodule_initialized(path)) {
+		strbuf_reset(&sb);
+		strbuf_addf(&sb, "submodule.%s.active", sub->name);
+		git_config_set_gently(sb.buf, "true");
+	}
+
+	/*
 	 * Copy url setting when it is not set yet.
 	 * To look up the url in .git/config, we must not fall back to
 	 * .gitmodules, so look it up directly.
@@ -420,6 +455,13 @@ static int module_init(int argc, const char **argv, const char *prefix)
 	if (module_list_compute(argc, argv, prefix, &pathspec, &list) < 0)
 		return 1;
 
+	/*
+	 * If there are no path args and submodule.active is set then,
+	 * by default, only initialize 'active' modules.
+	 */
+	if (!argc && git_config_get_value_multi("submodule.active"))
+		module_list_active(&list);
+
 	for (i = 0; i < list.nr; i++)
 		init_submodule(list.entries[i]->name, prefix, quiet);
 
@@ -577,9 +619,7 @@ static int module_clone(int argc, const char **argv, const char *prefix)
 	const char *name = NULL, *url = NULL, *depth = NULL;
 	int quiet = 0;
 	int progress = 0;
-	FILE *submodule_dot_git;
 	char *p, *path = NULL, *sm_gitdir;
-	struct strbuf rel_path = STRBUF_INIT;
 	struct strbuf sb = STRBUF_INIT;
 	struct string_list reference = STRING_LIST_INIT_NODUP;
 	char *sm_alternate = NULL, *error_strategy = NULL;
@@ -651,27 +691,12 @@ static int module_clone(int argc, const char **argv, const char *prefix)
 		strbuf_reset(&sb);
 	}
 
-	/* Write a .git file in the submodule to redirect to the superproject. */
-	strbuf_addf(&sb, "%s/.git", path);
-	if (safe_create_leading_directories_const(sb.buf) < 0)
-		die(_("could not create leading directories of '%s'"), sb.buf);
-	submodule_dot_git = fopen(sb.buf, "w");
-	if (!submodule_dot_git)
-		die_errno(_("cannot open file '%s'"), sb.buf);
-
-	fprintf_or_die(submodule_dot_git, "gitdir: %s\n",
-		       relative_path(sm_gitdir, path, &rel_path));
-	if (fclose(submodule_dot_git))
-		die(_("could not close file %s"), sb.buf);
-	strbuf_reset(&sb);
-	strbuf_reset(&rel_path);
+	/* Connect module worktree and git dir */
+	connect_work_tree_and_git_dir(path, sm_gitdir);
 
-	/* Redirect the worktree of the submodule in the superproject's config */
 	p = git_pathdup_submodule(path, "config");
 	if (!p)
 		die(_("could not get submodule directory for '%s'"), path);
-	git_config_set_in_file(p, "core.worktree",
-			       relative_path(path, sm_gitdir, &rel_path));
 
 	/* setup alternateLocation and alternateErrorStrategy in the cloned submodule if needed */
 	git_config_get_string("submodule.alternateLocation", &sm_alternate);
@@ -687,7 +712,6 @@ static int module_clone(int argc, const char **argv, const char *prefix)
 	free(error_strategy);
 
 	strbuf_release(&sb);
-	strbuf_release(&rel_path);
 	free(sm_gitdir);
 	free(path);
 	free(p);
@@ -759,7 +783,6 @@ static int prepare_to_clone_next_submodule(const struct cache_entry *ce,
 	struct strbuf displaypath_sb = STRBUF_INIT;
 	struct strbuf sb = STRBUF_INIT;
 	const char *displaypath = NULL;
-	char *url = NULL;
 	int needs_cloning = 0;
 
 	if (ce_stage(ce)) {
@@ -793,15 +816,8 @@ static int prepare_to_clone_next_submodule(const struct cache_entry *ce,
 		goto cleanup;
 	}
 
-	/*
-	 * Looking up the url in .git/config.
-	 * We must not fall back to .gitmodules as we only want
-	 * to process configured submodules.
-	 */
-	strbuf_reset(&sb);
-	strbuf_addf(&sb, "submodule.%s.url", sub->name);
-	git_config_get_string(sb.buf, &url);
-	if (!url) {
+	/* Check if the submodule has been initialized. */
+	if (!is_submodule_initialized(ce->name)) {
 		next_submodule_warn_missing(suc, out, displaypath);
 		goto cleanup;
 	}
@@ -835,7 +851,7 @@ static int prepare_to_clone_next_submodule(const struct cache_entry *ce,
 		argv_array_push(&child->args, "--depth=1");
 	argv_array_pushl(&child->args, "--path", sub->path, NULL);
 	argv_array_pushl(&child->args, "--name", sub->name, NULL);
-	argv_array_pushl(&child->args, "--url", url, NULL);
+	argv_array_pushl(&child->args, "--url", sub->url, NULL);
 	if (suc->references.nr) {
 		struct string_list_item *item;
 		for_each_string_list_item(item, &suc->references)
@@ -845,7 +861,6 @@ static int prepare_to_clone_next_submodule(const struct cache_entry *ce,
 		argv_array_push(&child->args, suc->depth);
 
 cleanup:
-	free(url);
 	strbuf_reset(&displaypath_sb);
 	strbuf_reset(&sb);
 
@@ -1127,6 +1142,16 @@ static int absorb_git_dirs(int argc, const char **argv, const char *prefix)
 	return 0;
 }
 
+static int is_active(int argc, const char **argv, const char *prefix)
+{
+	if (argc != 2)
+		die("submodule--helper is-active takes exactly 1 arguments");
+
+	gitmodules_config();
+
+	return !is_submodule_initialized(argv[1]);
+}
+
 #define SUPPORT_SUPER_PREFIX (1<<0)
 
 struct cmd_struct {
@@ -1146,6 +1171,7 @@ static struct cmd_struct commands[] = {
 	{"init", module_init, SUPPORT_SUPER_PREFIX},
 	{"remote-branch", resolve_remote_submodule_branch, 0},
 	{"absorb-git-dirs", absorb_git_dirs, SUPPORT_SUPER_PREFIX},
+	{"is-active", is_active, 0},
 };
 
 int cmd_submodule__helper(int argc, const char **argv, const char *prefix)
diff --git a/builtin/tag.c b/builtin/tag.c
index ad29be6923..dbc6f5b74b 100644
--- a/builtin/tag.c
+++ b/builtin/tag.c
@@ -22,7 +22,7 @@
 static const char * const git_tag_usage[] = {
 	N_("git tag [-a | -s | -u <key-id>] [-f] [-m <msg> | -F <file>] <tagname> [<head>]"),
 	N_("git tag -d <tagname>..."),
-	N_("git tag -l [-n[<num>]] [--contains <commit>] [--points-at <object>]"
+	N_("git tag -l [-n[<num>]] [--contains <commit>] [--no-contains <commit>] [--points-at <object>]"
 		"\n\t\t[--format=<format>] [--[no-]merged [<commit>]] [<pattern>...]"),
 	N_("git tag -v [--format=<format>] <tagname>..."),
 	NULL
@@ -424,14 +424,17 @@ int cmd_tag(int argc, const char **argv, const char *prefix)
 		OPT_GROUP(N_("Tag listing options")),
 		OPT_COLUMN(0, "column", &colopts, N_("show tag list in columns")),
 		OPT_CONTAINS(&filter.with_commit, N_("print only tags that contain the commit")),
+		OPT_NO_CONTAINS(&filter.no_commit, N_("print only tags that don't contain the commit")),
 		OPT_WITH(&filter.with_commit, N_("print only tags that contain the commit")),
+		OPT_WITHOUT(&filter.no_commit, N_("print only tags that don't contain the commit")),
 		OPT_MERGED(&filter, N_("print only tags that are merged")),
 		OPT_NO_MERGED(&filter, N_("print only tags that are not merged")),
 		OPT_CALLBACK(0 , "sort", sorting_tail, N_("key"),
 			     N_("field name to sort on"), &parse_opt_ref_sorting),
 		{
 			OPTION_CALLBACK, 0, "points-at", &filter.points_at, N_("object"),
-			N_("print only tags of the object"), 0, parse_opt_object_name
+			N_("print only tags of the object"), PARSE_OPT_LASTARG_DEFAULT,
+			parse_opt_object_name, (intptr_t) "HEAD"
 		},
 		OPT_STRING(  0 , "format", &format, N_("format"), N_("format to use for the output")),
 		OPT_BOOL('i', "ignore-case", &icase, N_("sorting and filtering are case insensitive")),
@@ -454,8 +457,14 @@ int cmd_tag(int argc, const char **argv, const char *prefix)
 	}
 	create_tag_object = (opt.sign || annotate || msg.given || msgfile);
 
-	if (argc == 0 && !cmdmode)
-		cmdmode = 'l';
+	if (!cmdmode) {
+		if (argc == 0)
+			cmdmode = 'l';
+		else if (filter.with_commit || filter.no_commit ||
+			 filter.points_at.nr || filter.merge_commit ||
+			 filter.lines != -1)
+			cmdmode = 'l';
+	}
 
 	if ((create_tag_object || force) && (cmdmode != 0))
 		usage_with_options(git_tag_usage, options);
@@ -485,13 +494,15 @@ int cmd_tag(int argc, const char **argv, const char *prefix)
 		return ret;
 	}
 	if (filter.lines != -1)
-		die(_("-n option is only allowed with -l."));
+		die(_("-n option is only allowed in list mode"));
 	if (filter.with_commit)
-		die(_("--contains option is only allowed with -l."));
+		die(_("--contains option is only allowed in list mode"));
+	if (filter.no_commit)
+		die(_("--no-contains option is only allowed in list mode"));
 	if (filter.points_at.nr)
-		die(_("--points-at option is only allowed with -l."));
+		die(_("--points-at option is only allowed in list mode"));
 	if (filter.merge_commit)
-		die(_("--merged and --no-merged option are only allowed with -l"));
+		die(_("--merged and --no-merged options are only allowed in list mode"));
 	if (cmdmode == 'd')
 		return for_each_tag_name(argv, delete_tag, NULL);
 	if (cmdmode == 'v') {
diff --git a/builtin/update-index.c b/builtin/update-index.c
index d74d72cc7f..ebfc09faa0 100644
--- a/builtin/update-index.c
+++ b/builtin/update-index.c
@@ -125,12 +125,16 @@ static int test_if_untracked_cache_is_supported(void)
 	struct stat st;
 	struct stat_data base;
 	int fd, ret = 0;
+	char *cwd;
 
 	strbuf_addstr(&mtime_dir, "mtime-test-XXXXXX");
 	if (!mkdtemp(mtime_dir.buf))
 		die_errno("Could not make temporary directory");
 
-	fprintf(stderr, _("Testing mtime in '%s' "), xgetcwd());
+	cwd = xgetcwd();
+	fprintf(stderr, _("Testing mtime in '%s' "), cwd);
+	free(cwd);
+
 	atexit(remove_test_directory);
 	xstat_mtime_dir(&st);
 	fill_stat_data(&base, &st);