patch, 6 partssparse-checkout: make set subsume init

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index d0f5c4702be..8612328e5dd 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -525,7 +525,8 @@ static struct sparse_checkout_set_opts {
 } set_opts;
 
 static void add_patterns_from_input(struct pattern_list *pl,
-				    int argc, const char **argv)
+				    int argc, const char **argv,
+				    int use_stdin)
 {
 	int i;
 	if (core_sparse_checkout_cone) {
@@ -535,7 +536,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 		hashmap_init(&pl->parent_hashmap, pl_hashmap_cmp, NULL, 0);
 		pl->use_cone_patterns = 1;
 
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf unquoted = STRBUF_INIT;
 			while (!strbuf_getline(&line, stdin)) {
 				if (line.buf[0] == '"') {
@@ -559,7 +560,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 			}
 		}
 	} else {
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf line = STRBUF_INIT;
 
 			while (!strbuf_getline(&line, stdin)) {
@@ -580,7 +581,8 @@ enum modify_type {
 };
 
 static void add_patterns_cone_mode(int argc, const char **argv,
-				   struct pattern_list *pl)
+				   struct pattern_list *pl,
+				   int use_stdin)
 {
 	struct strbuf buffer = STRBUF_INIT;
 	struct pattern_entry *pe;
@@ -588,7 +590,7 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 	struct pattern_list existing;
 	char *sparse_filename = get_sparse_checkout_filename();
 
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 
 	memset(&existing, 0, sizeof(existing));
 	existing.use_cone_patterns = core_sparse_checkout_cone;
@@ -614,17 +616,19 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 }
 
 static void add_patterns_literal(int argc, const char **argv,
-				 struct pattern_list *pl)
+				 struct pattern_list *pl,
+				 int use_stdin)
 {
 	char *sparse_filename = get_sparse_checkout_filename();
 	if (add_patterns_from_file_to_list(sparse_filename, "", 0,
 					   pl, NULL, 0))
 		die(_("unable to load existing sparse-checkout patterns"));
 	free(sparse_filename);
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 }
 
-static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
+static int modify_pattern_list(int argc, const char **argv, int use_stdin,
+			       enum modify_type m)
 {
 	int result;
 	int changed_config = 0;
@@ -633,13 +637,13 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 	switch (m) {
 	case ADD:
 		if (core_sparse_checkout_cone)
-			add_patterns_cone_mode(argc, argv, pl);
+			add_patterns_cone_mode(argc, argv, pl, use_stdin);
 		else
-			add_patterns_literal(argc, argv, pl);
+			add_patterns_literal(argc, argv, pl, use_stdin);
 		break;
 
 	case REPLACE:
-		add_patterns_from_input(pl, argc, argv);
+		add_patterns_from_input(pl, argc, argv, use_stdin);
 		break;
 	}
 
@@ -675,7 +679,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 8612328e5dd..e252b82136e 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -515,15 +515,6 @@ static void strbuf_to_cone_pattern(struct strbuf *line, struct pattern_list *pl)
 	insert_recursive_pattern(pl, line);
 }
 
-static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout (set|add) (--stdin | <patterns>)"),
-	NULL
-};
-
-static struct sparse_checkout_set_opts {
-	int use_stdin;
-} set_opts;
-
 static void add_patterns_from_input(struct pattern_list *pl,
 				    int argc, const char **argv,
 				    int use_stdin)
@@ -663,8 +654,43 @@ static int modify_pattern_list(int argc, const char **argv, int use_stdin,
 	return result;
 }
 
-static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
-			       enum modify_type m)
+static char const * const builtin_sparse_checkout_add_usage[] = {
+	N_("git sparse-checkout add (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_add_opts {
+	int use_stdin;
+} add_opts;
+
+static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
+{
+	static struct option builtin_sparse_checkout_add_options[] = {
+		OPT_BOOL(0, "stdin", &add_opts.use_stdin,
+			 N_("read patterns from standard in")),
+		OPT_END(),
+	};
+
+	repo_read_index(the_repository);
+
+	argc = parse_options(argc, argv, prefix,
+			     builtin_sparse_checkout_add_options,
+			     builtin_sparse_checkout_add_usage,
+			     PARSE_OPT_KEEP_UNKNOWN);
+
+	return modify_pattern_list(argc, argv, add_opts.use_stdin, ADD);
+}
+
+static char const * const builtin_sparse_checkout_set_usage[] = {
+	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_set_opts {
+	int use_stdin;
+} set_opts;
+
+static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
 	static struct option builtin_sparse_checkout_set_options[] = {
 		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
@@ -679,7 +705,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {
@@ -762,9 +788,9 @@ int cmd_sparse_checkout(int argc, const char **argv, const char *prefix)
 		if (!strcmp(argv[0], "init"))
 			return sparse_checkout_init(argc, argv);
 		if (!strcmp(argv[0], "set"))
-			return sparse_checkout_set(argc, argv, prefix, REPLACE);
+			return sparse_checkout_set(argc, argv, prefix);
 		if (!strcmp(argv[0], "add"))
-			return sparse_checkout_set(argc, argv, prefix, ADD);
+			return sparse_checkout_add(argc, argv, prefix);
 		if (!strcmp(argv[0], "reapply"))
 			return sparse_checkout_reapply(argc, argv);
 		if (!strcmp(argv[0], "disable"))

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index e252b82136e..cf6a6c6c3a7 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -682,17 +682,26 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 }
 
 static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	N_("git sparse-checkout set [--cone] [--[no-]sparse-index] (--stdin | <patterns>)"),
 	NULL
 };
 
 static struct sparse_checkout_set_opts {
+	int cone_mode;
+	int sparse_index;
 	int use_stdin;
 } set_opts;
 
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
+	int mode, record_mode;
+	const char *default_patterns[] = {"/*", "!/*/"};
+
 	static struct option builtin_sparse_checkout_set_options[] = {
+		OPT_BOOL(0, "cone", &set_opts.cone_mode,
+			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &set_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
 			 N_("read patterns from standard in")),
 		OPT_END(),
@@ -700,11 +709,52 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 
 	repo_read_index(the_repository);
 
+	set_opts.cone_mode = -1;
+	set_opts.sparse_index = -1;
+
 	argc = parse_options(argc, argv, prefix,
 			     builtin_sparse_checkout_set_options,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
+	/* Determine if we need to record the mode; ensure sparse checkout on */
+	record_mode = (set_opts.cone_mode != -1) || !core_apply_sparse_checkout;
+	core_apply_sparse_checkout = 1;
+
+	/* If not specified, use previous definition of cone mode */
+	if (set_opts.cone_mode == -1 && core_apply_sparse_checkout)
+		set_opts.cone_mode = core_sparse_checkout_cone;
+
+	/* Set cone/non-cone mode appropriately */
+	if (set_opts.cone_mode == 1) {
+		mode = MODE_CONE_PATTERNS;
+		core_sparse_checkout_cone = 1;
+	} else {
+		mode = MODE_ALL_PATTERNS;
+	}
+	if (record_mode && set_config(mode))
+		return 1;
+
+	/* Set sparse-index/non-sparse-index mode if specified */
+	if (set_opts.sparse_index >= 0) {
+		if (set_sparse_index_config(the_repository, set_opts.sparse_index) < 0)
+			die(_("failed to modify sparse-index config"));
+
+		/* force an index rewrite */
+		repo_read_index(the_repository);
+		the_repository->index->updated_workdir = 1;
+	}
+
+	/*
+	 * Cone mode automatically specifies the toplevel directory.  For
+	 * non-cone mode, if nothing is specified, manually select just the
+	 * top-level directory (much as 'init' would do).
+	 */
+	if (!core_sparse_checkout_cone && argc == 0) {
+		argv = default_patterns;
+		argc = 2;
+	}
+
 	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 

diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index 42056ee9ff9..d22c925ecf8 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -30,28 +30,35 @@ COMMANDS
 'list'::
 	Describe the patterns in the sparse-checkout file.
 
-'init'::
-	Enable the `core.sparseCheckout` setting. If the
-	sparse-checkout file does not exist, then populate it with
-	patterns that match every file in the root directory and
-	no other directories, then will remove all directories tracked
-	by Git. Add patterns to the sparse-checkout file to
-	repopulate the working directory.
+'set'::
+	Enable the necessary config settings
+	(extensions.worktreeConfig, core.sparseCheckout,
+	core.sparseCheckoutCone) if they are not already enabled, and
+	write a set of patterns to the sparse-checkout file from the
+	list of arguments following the 'set' subcommand. Update the
+	working directory to match the new patterns.
 +
-To avoid interfering with other worktrees, it first enables the
-`extensions.worktreeConfig` setting and makes sure to set the
-`core.sparseCheckout` setting in the worktree-specific config file.
+When the `--stdin` option is provided, the patterns are read from
+standard in as a newline-delimited list instead of from the arguments.
 +
-When `--cone` is provided, the `core.sparseCheckoutCone` setting is
-also set, allowing for better performance with a limited set of
-patterns (see 'CONE PATTERN SET' below).
+When `--cone` is passed or `core.sparseCheckoutCone` is enabled, the
+input list is considered a list of directories instead of
+sparse-checkout patterns.  This allows for better performance with a
+limited set of patterns (see 'CONE PATTERN SET' below).  Note that the
+set command will write patterns to the sparse-checkout file to include
+all files contained in those directories (recursively) as well as
+files that are siblings of ancestor directories. The input format
+matches the output of `git ls-tree --name-only`.  This includes
+interpreting pathnames that begin with a double quote (") as C-style
+quoted strings.
 +
-Use the `--[no-]sparse-index` option to toggle the use of the sparse
-index format. This reduces the size of the index to be more closely
-aligned with your sparse-checkout definition. This can have significant
-performance advantages for commands such as `git status` or `git add`.
-This feature is still experimental. Some commands might be slower with
-a sparse index until they are properly integrated with the feature.
+Use the `--[no-]sparse-index` option to use a sparse index (the
+default is to not use it).  A sparse index reduces the size of the
+index to be more closely aligned with your sparse-checkout
+definition. This can have significant performance advantages for
+commands such as `git status` or `git add`.  This feature is still
+experimental. Some commands might be slower with a sparse index until
+they are properly integrated with the feature.
 +
 **WARNING:** Using a sparse index requires modifying the index in a way
 that is not completely understood by external tools. If you have trouble
@@ -60,23 +67,6 @@ to rewrite your index to not be sparse. Older versions of Git will not
 understand the sparse directory entries index extension and may fail to
 interact with your repository until it is disabled.
 
-'set'::
-	Write a set of patterns to the sparse-checkout file, as given as
-	a list of arguments following the 'set' subcommand. Update the
-	working directory to match the new patterns. Enable the
-	core.sparseCheckout config setting if it is not already enabled.
-+
-When the `--stdin` option is provided, the patterns are read from
-standard in as a newline-delimited list instead of from the arguments.
-+
-When `core.sparseCheckoutCone` is enabled, the input list is considered a
-list of directories instead of sparse-checkout patterns. The command writes
-patterns to the sparse-checkout file to include all files contained in those
-directories (recursively) as well as files that are siblings of ancestor
-directories. The input format matches the output of `git ls-tree --name-only`.
-This includes interpreting pathnames that begin with a double quote (") as
-C-style quoted strings.
-
 'add'::
 	Update the sparse-checkout file to include additional patterns.
 	By default, these patterns are read from the command-line arguments,
@@ -96,9 +86,27 @@ C-style quoted strings.
 
 'disable'::
 	Disable the `core.sparseCheckout` config setting, and restore the
-	working directory to include all files. Leaves the sparse-checkout
-	file intact so a later 'git sparse-checkout init' command may
-	return the working directory to the same state.
+	working directory to include all files.
+
+'init'::
+	Deprecated command that behaves like `set` with no specified paths.
+	May be removed in the future.
++
+Historically, `set` did not used to handle all the necessary config
+settings, which meant that both `init` and `set` had to be called.
+Invoking both meant the `init` step would first remove nearly all
+tracked files (and in cone mode, ignored files too), then the `set`
+step would add many of the tracked files (but not ignored files) back.
+In addition to the lost files, the performance and UI of this
+combination was poor.
++
+Also, historically, `init` would not actually initialize the
+sparse-checkout file if it already existed.  This meant it was
+possible to return to a sparse-checkout without remembering which
+paths to pass to a subsequent 'set' or 'add' command.  However,
+`--cone` and `--sparse-index` options would not be remembered across
+the disable command, so the easy restore of calling a plain `init`
+decreased in utility.
 
 SPARSE CHECKOUT
 ---------------
@@ -117,10 +125,8 @@ directory, it updates the skip-worktree bits in the index based
 on this file. The files matching the patterns in the file will
 appear in the working directory, and the rest will not.
 
-To enable the sparse-checkout feature, run `git sparse-checkout init` to
-initialize a simple sparse-checkout file and enable the `core.sparseCheckout`
-config setting. Then, run `git sparse-checkout set` to modify the patterns in
-the sparse-checkout file.
+To enable the sparse-checkout feature, run `git sparse-checkout set` to
+set the patterns you want to use.
 
 To repopulate the working directory with all files, use the
 `git sparse-checkout disable` command.

Documentation/git-clone.txt, Documentation/git-sparse-checkout.txt

diff --git a/Documentation/git-clone.txt b/Documentation/git-clone.txt
index 3fe3810f1ce..b348a71fc68 100644
--- a/Documentation/git-clone.txt
+++ b/Documentation/git-clone.txt
@@ -167,10 +167,10 @@ objects from the source repository into a pack in the cloned repository.
 	configuration variables are created.
 
 --sparse::
-	Initialize the sparse-checkout file so the working
-	directory starts with only the files in the root
-	of the repository. The sparse-checkout file can be
-	modified to grow the working directory as needed.
+	Employ a sparse-checkout, with only files in the toplevel
+	directory initially being present.  The
+	linkgit:git-sparse-checkout[1] command can be used to grow the
+	working directory as needed.
 
 --filter=<filter-spec>::
 	Use the partial clone feature and request that the server sends
diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index d22c925ecf8..73e7645b77a 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -115,7 +115,7 @@ SPARSE CHECKOUT
 It uses the skip-worktree bit (see linkgit:git-update-index[1]) to tell
 Git whether a file in the working directory is worth looking at. If
 the skip-worktree bit is set, then the file is ignored in the working
-directory. Git will not populate the contents of those files, which
+directory. Git will avoid populating the contents of those files, which
 makes a sparse checkout helpful when working in a repository with many
 files, but only a few are important to the current user.
 

diff --git a/builtin/clone.c b/builtin/clone.c
index fb377b27657..5bed37f8b51 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -633,7 +633,7 @@ static int git_sparse_checkout_init(const char *repo)
 {
 	struct strvec argv = STRVEC_INIT;
 	int result = 0;
-	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "init", NULL);
+	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "set", NULL);
 
 	/*
 	 * We must apply the setting in the current process

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index d0f5c4702be..8612328e5dd 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -525,7 +525,8 @@ static struct sparse_checkout_set_opts {
 } set_opts;
 
 static void add_patterns_from_input(struct pattern_list *pl,
-				    int argc, const char **argv)
+				    int argc, const char **argv,
+				    int use_stdin)
 {
 	int i;
 	if (core_sparse_checkout_cone) {
@@ -535,7 +536,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 		hashmap_init(&pl->parent_hashmap, pl_hashmap_cmp, NULL, 0);
 		pl->use_cone_patterns = 1;
 
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf unquoted = STRBUF_INIT;
 			while (!strbuf_getline(&line, stdin)) {
 				if (line.buf[0] == '"') {
@@ -559,7 +560,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 			}
 		}
 	} else {
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf line = STRBUF_INIT;
 
 			while (!strbuf_getline(&line, stdin)) {
@@ -580,7 +581,8 @@ enum modify_type {
 };
 
 static void add_patterns_cone_mode(int argc, const char **argv,
-				   struct pattern_list *pl)
+				   struct pattern_list *pl,
+				   int use_stdin)
 {
 	struct strbuf buffer = STRBUF_INIT;
 	struct pattern_entry *pe;
@@ -588,7 +590,7 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 	struct pattern_list existing;
 	char *sparse_filename = get_sparse_checkout_filename();
 
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 
 	memset(&existing, 0, sizeof(existing));
 	existing.use_cone_patterns = core_sparse_checkout_cone;
@@ -614,17 +616,19 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 }
 
 static void add_patterns_literal(int argc, const char **argv,
-				 struct pattern_list *pl)
+				 struct pattern_list *pl,
+				 int use_stdin)
 {
 	char *sparse_filename = get_sparse_checkout_filename();
 	if (add_patterns_from_file_to_list(sparse_filename, "", 0,
 					   pl, NULL, 0))
 		die(_("unable to load existing sparse-checkout patterns"));
 	free(sparse_filename);
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 }
 
-static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
+static int modify_pattern_list(int argc, const char **argv, int use_stdin,
+			       enum modify_type m)
 {
 	int result;
 	int changed_config = 0;
@@ -633,13 +637,13 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 	switch (m) {
 	case ADD:
 		if (core_sparse_checkout_cone)
-			add_patterns_cone_mode(argc, argv, pl);
+			add_patterns_cone_mode(argc, argv, pl, use_stdin);
 		else
-			add_patterns_literal(argc, argv, pl);
+			add_patterns_literal(argc, argv, pl, use_stdin);
 		break;
 
 	case REPLACE:
-		add_patterns_from_input(pl, argc, argv);
+		add_patterns_from_input(pl, argc, argv, use_stdin);
 		break;
 	}
 
@@ -675,7 +679,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 8612328e5dd..e252b82136e 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -515,15 +515,6 @@ static void strbuf_to_cone_pattern(struct strbuf *line, struct pattern_list *pl)
 	insert_recursive_pattern(pl, line);
 }
 
-static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout (set|add) (--stdin | <patterns>)"),
-	NULL
-};
-
-static struct sparse_checkout_set_opts {
-	int use_stdin;
-} set_opts;
-
 static void add_patterns_from_input(struct pattern_list *pl,
 				    int argc, const char **argv,
 				    int use_stdin)
@@ -663,8 +654,43 @@ static int modify_pattern_list(int argc, const char **argv, int use_stdin,
 	return result;
 }
 
-static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
-			       enum modify_type m)
+static char const * const builtin_sparse_checkout_add_usage[] = {
+	N_("git sparse-checkout add (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_add_opts {
+	int use_stdin;
+} add_opts;
+
+static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
+{
+	static struct option builtin_sparse_checkout_add_options[] = {
+		OPT_BOOL(0, "stdin", &add_opts.use_stdin,
+			 N_("read patterns from standard in")),
+		OPT_END(),
+	};
+
+	repo_read_index(the_repository);
+
+	argc = parse_options(argc, argv, prefix,
+			     builtin_sparse_checkout_add_options,
+			     builtin_sparse_checkout_add_usage,
+			     PARSE_OPT_KEEP_UNKNOWN);
+
+	return modify_pattern_list(argc, argv, add_opts.use_stdin, ADD);
+}
+
+static char const * const builtin_sparse_checkout_set_usage[] = {
+	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_set_opts {
+	int use_stdin;
+} set_opts;
+
+static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
 	static struct option builtin_sparse_checkout_set_options[] = {
 		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
@@ -679,7 +705,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {
@@ -762,9 +788,9 @@ int cmd_sparse_checkout(int argc, const char **argv, const char *prefix)
 		if (!strcmp(argv[0], "init"))
 			return sparse_checkout_init(argc, argv);
 		if (!strcmp(argv[0], "set"))
-			return sparse_checkout_set(argc, argv, prefix, REPLACE);
+			return sparse_checkout_set(argc, argv, prefix);
 		if (!strcmp(argv[0], "add"))
-			return sparse_checkout_set(argc, argv, prefix, ADD);
+			return sparse_checkout_add(argc, argv, prefix);
 		if (!strcmp(argv[0], "reapply"))
 			return sparse_checkout_reapply(argc, argv);
 		if (!strcmp(argv[0], "disable"))

builtin/sparse-checkout.c, t/t1091-sparse-checkout-builtin.sh

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index e252b82136e..e9f644ac362 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -56,6 +56,9 @@ static int sparse_checkout_list(int argc, const char **argv)
 	char *sparse_filename;
 	int res;
 
+	if (!core_apply_sparse_checkout)
+		die(_("this worktree is not sparse"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_list_options,
 			     builtin_sparse_checkout_list_usage, 0);
@@ -671,6 +674,9 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 		OPT_END(),
 	};
 
+	if (!core_apply_sparse_checkout)
+		die(_("no sparse-checkout to add to"));
+
 	repo_read_index(the_repository);
 
 	argc = parse_options(argc, argv, prefix,
@@ -719,6 +725,9 @@ static int sparse_checkout_reapply(int argc, const char **argv)
 		OPT_END(),
 	};
 
+	if (!core_apply_sparse_checkout)
+		die(_("must be in a sparse-checkout to reapply sparsity patterns"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_reapply_options,
 			     builtin_sparse_checkout_reapply_usage, 0);
@@ -740,6 +749,9 @@ static int sparse_checkout_disable(int argc, const char **argv)
 	struct pattern_list pl;
 	struct strbuf match_all = STRBUF_INIT;
 
+	if (!core_apply_sparse_checkout)
+		die(_("no active sparse-checkout to disable"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_disable_options,
 			     builtin_sparse_checkout_disable_usage, 0);
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 272ba1b566b..90a281bcf64 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -41,7 +41,15 @@ test_expect_success 'setup' '
 	)
 '
 
-test_expect_success 'git sparse-checkout list (empty)' '
+test_expect_success 'git sparse-checkout list (not sparse)' '
+	test_must_fail git -C repo sparse-checkout list >list 2>err &&
+	test_must_be_empty list &&
+	test_i18ngrep "this worktree is not sparse" err
+'
+
+test_expect_success 'git sparse-checkout list (not sparse)' '
+	git -C repo sparse-checkout set &&
+	rm repo/.git/info/sparse-checkout &&
 	git -C repo sparse-checkout list >list 2>err &&
 	test_must_be_empty list &&
 	test_i18ngrep "this worktree is not sparse (sparse-checkout file may not exist)" err

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index e9f644ac362..0ee28f48134 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -699,8 +699,9 @@ static struct sparse_checkout_set_opts {
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
 	static struct option builtin_sparse_checkout_set_options[] = {
-		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
-			 N_("read patterns from standard in")),
+		OPT_BOOL_F(0, "stdin", &set_opts.use_stdin,
+			   N_("read patterns from standard in"),
+			   PARSE_OPT_NONEG),
 		OPT_END(),
 	};
 

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 0ee28f48134..f176435b6be 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -383,6 +383,41 @@ static int set_config(enum sparse_checkout_mode mode)
 	return 0;
 }
 
+static int update_modes(int *cone_mode, int *sparse_index)
+{
+	int mode, record_mode;
+
+	/* Determine if we need to record the mode; ensure sparse checkout on */
+	record_mode = (*cone_mode != -1) || !core_apply_sparse_checkout;
+
+	/* If not specified, use previous definition of cone mode */
+	if (*cone_mode == -1 && core_apply_sparse_checkout)
+		*cone_mode = core_sparse_checkout_cone;
+
+	/* Set cone/non-cone mode appropriately */
+	core_apply_sparse_checkout = 1;
+	if (*cone_mode == 1) {
+		mode = MODE_CONE_PATTERNS;
+		core_sparse_checkout_cone = 1;
+	} else {
+		mode = MODE_ALL_PATTERNS;
+	}
+	if (record_mode && set_config(mode))
+		return 1;
+
+	/* Set sparse-index/non-sparse-index mode if specified */
+	if (*sparse_index >= 0) {
+		if (set_sparse_index_config(the_repository, *sparse_index) < 0)
+			die(_("failed to modify sparse-index config"));
+
+		/* force an index rewrite */
+		repo_read_index(the_repository);
+		the_repository->index->updated_workdir = 1;
+	}
+
+	return 0;
+}
+
 static char const * const builtin_sparse_checkout_init_usage[] = {
 	N_("git sparse-checkout init [--cone] [--[no-]sparse-index]"),
 	NULL
@@ -399,7 +434,6 @@ static int sparse_checkout_init(int argc, const char **argv)
 	char *sparse_filename;
 	int res;
 	struct object_id oid;
-	int mode;
 	struct strbuf pattern = STRBUF_INIT;
 
 	static struct option builtin_sparse_checkout_init_options[] = {
@@ -412,19 +446,14 @@ static int sparse_checkout_init(int argc, const char **argv)
 
 	repo_read_index(the_repository);
 
+	init_opts.cone_mode = -1;
 	init_opts.sparse_index = -1;
 
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_init_options,
 			     builtin_sparse_checkout_init_usage, 0);
 
-	if (init_opts.cone_mode) {
-		mode = MODE_CONE_PATTERNS;
-		core_sparse_checkout_cone = 1;
-	} else
-		mode = MODE_ALL_PATTERNS;
-
-	if (set_config(mode))
+	if (update_modes(&init_opts.cone_mode, &init_opts.sparse_index))
 		return 1;
 
 	memset(&pl, 0, sizeof(pl));
@@ -432,17 +461,6 @@ static int sparse_checkout_init(int argc, const char **argv)
 	sparse_filename = get_sparse_checkout_filename();
 	res = add_patterns_from_file_to_list(sparse_filename, "", 0, &pl, NULL, 0);
 
-	if (init_opts.sparse_index >= 0) {
-		if (set_sparse_index_config(the_repository, init_opts.sparse_index) < 0)
-			die(_("failed to modify sparse-index config"));
-
-		/* force an index rewrite */
-		repo_read_index(the_repository);
-		the_repository->index->updated_workdir = 1;
-	}
-
-	core_apply_sparse_checkout = 1;
-
 	/* If we already have a sparse-checkout file, use it. */
 	if (res >= 0) {
 		free(sparse_filename);

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index f176435b6be..1ecdc3ddd5a 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -706,17 +706,26 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 }
 
 static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	N_("git sparse-checkout set [--[no-]cone] [--[no-]sparse-index] (--stdin | <patterns>)"),
 	NULL
 };
 
 static struct sparse_checkout_set_opts {
+	int cone_mode;
+	int sparse_index;
 	int use_stdin;
 } set_opts;
 
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
+	int default_patterns_nr = 2;
+	const char *default_patterns[] = {"/*", "!/*/", NULL};
+
 	static struct option builtin_sparse_checkout_set_options[] = {
+		OPT_BOOL(0, "cone", &set_opts.cone_mode,
+			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &set_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_BOOL_F(0, "stdin", &set_opts.use_stdin,
 			   N_("read patterns from standard in"),
 			   PARSE_OPT_NONEG),
@@ -725,11 +734,27 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 
 	repo_read_index(the_repository);
 
+	set_opts.cone_mode = -1;
+	set_opts.sparse_index = -1;
+
 	argc = parse_options(argc, argv, prefix,
 			     builtin_sparse_checkout_set_options,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
+	if (update_modes(&set_opts.cone_mode, &set_opts.sparse_index))
+		return 1;
+
+	/*
+	 * Cone mode automatically specifies the toplevel directory.  For
+	 * non-cone mode, if nothing is specified, manually select just the
+	 * top-level directory (much as 'init' would do).
+	 */
+	if (!core_sparse_checkout_cone && argc == 0) {
+		argv = default_patterns;
+		argc = default_patterns_nr;
+	}
+
 	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 1ecdc3ddd5a..9d2a05677c4 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -759,13 +759,22 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {
-	N_("git sparse-checkout reapply"),
+	N_("git sparse-checkout reapply [--[no-]cone] [--[no-]sparse-index] "),
 	NULL
 };
 
+static struct sparse_checkout_reapply_opts {
+	int cone_mode;
+	int sparse_index;
+} reapply_opts;
+
 static int sparse_checkout_reapply(int argc, const char **argv)
 {
 	static struct option builtin_sparse_checkout_reapply_options[] = {
+		OPT_BOOL(0, "cone", &reapply_opts.cone_mode,
+			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &reapply_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_END(),
 	};
 
@@ -777,6 +786,13 @@ static int sparse_checkout_reapply(int argc, const char **argv)
 			     builtin_sparse_checkout_reapply_usage, 0);
 
 	repo_read_index(the_repository);
+
+	reapply_opts.cone_mode = -1;
+	reapply_opts.sparse_index = -1;
+
+	if (update_modes(&reapply_opts.cone_mode, &reapply_opts.sparse_index))
+		return 1;
+
 	return update_working_directory(NULL);
 }
 

diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index 42056ee9ff9..c7a25e282e7 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -30,28 +30,36 @@ COMMANDS
 'list'::
 	Describe the patterns in the sparse-checkout file.
 
-'init'::
-	Enable the `core.sparseCheckout` setting. If the
-	sparse-checkout file does not exist, then populate it with
-	patterns that match every file in the root directory and
-	no other directories, then will remove all directories tracked
-	by Git. Add patterns to the sparse-checkout file to
-	repopulate the working directory.
+'set'::
+	Enable the necessary config settings
+	(extensions.worktreeConfig, core.sparseCheckout,
+	core.sparseCheckoutCone) if they are not already enabled, and
+	write a set of patterns to the sparse-checkout file from the
+	list of arguments following the 'set' subcommand. Update the
+	working directory to match the new patterns.
 +
-To avoid interfering with other worktrees, it first enables the
-`extensions.worktreeConfig` setting and makes sure to set the
-`core.sparseCheckout` setting in the worktree-specific config file.
+When the `--stdin` option is provided, the patterns are read from
+standard in as a newline-delimited list instead of from the arguments.
 +
-When `--cone` is provided, the `core.sparseCheckoutCone` setting is
-also set, allowing for better performance with a limited set of
-patterns (see 'CONE PATTERN SET' below).
+When `--cone` is passed or `core.sparseCheckoutCone` is enabled, the
+input list is considered a list of directories instead of
+sparse-checkout patterns.  This allows for better performance with a
+limited set of patterns (see 'CONE PATTERN SET' below).  Note that the
+set command will write patterns to the sparse-checkout file to include
+all files contained in those directories (recursively) as well as
+files that are siblings of ancestor directories. The input format
+matches the output of `git ls-tree --name-only`.  This includes
+interpreting pathnames that begin with a double quote (") as C-style
+quoted strings.  This may become the default in the future; --no-cone
+can be passed to request non-cone mode.
 +
-Use the `--[no-]sparse-index` option to toggle the use of the sparse
-index format. This reduces the size of the index to be more closely
-aligned with your sparse-checkout definition. This can have significant
-performance advantages for commands such as `git status` or `git add`.
-This feature is still experimental. Some commands might be slower with
-a sparse index until they are properly integrated with the feature.
+Use the `--[no-]sparse-index` option to use a sparse index (the
+default is to not use it).  A sparse index reduces the size of the
+index to be more closely aligned with your sparse-checkout
+definition. This can have significant performance advantages for
+commands such as `git status` or `git add`.  This feature is still
+experimental. Some commands might be slower with a sparse index until
+they are properly integrated with the feature.
 +
 **WARNING:** Using a sparse index requires modifying the index in a way
 that is not completely understood by external tools. If you have trouble
@@ -60,23 +68,6 @@ to rewrite your index to not be sparse. Older versions of Git will not
 understand the sparse directory entries index extension and may fail to
 interact with your repository until it is disabled.
 
-'set'::
-	Write a set of patterns to the sparse-checkout file, as given as
-	a list of arguments following the 'set' subcommand. Update the
-	working directory to match the new patterns. Enable the
-	core.sparseCheckout config setting if it is not already enabled.
-+
-When the `--stdin` option is provided, the patterns are read from
-standard in as a newline-delimited list instead of from the arguments.
-+
-When `core.sparseCheckoutCone` is enabled, the input list is considered a
-list of directories instead of sparse-checkout patterns. The command writes
-patterns to the sparse-checkout file to include all files contained in those
-directories (recursively) as well as files that are siblings of ancestor
-directories. The input format matches the output of `git ls-tree --name-only`.
-This includes interpreting pathnames that begin with a double quote (") as
-C-style quoted strings.
-
 'add'::
 	Update the sparse-checkout file to include additional patterns.
 	By default, these patterns are read from the command-line arguments,
@@ -93,12 +84,35 @@ C-style quoted strings.
 	cases, it can make sense to run `git sparse-checkout reapply` later
 	after cleaning up affected paths (e.g. resolving conflicts, undoing
 	or committing changes, etc.).
++
+The `reapply` command can also take `--[no-]cone` and `--[no-]sparse-index`
+flags, with the same meaning as the flags from the `set` command, in order
+to change which sparsity mode you are using without needing to also respecify
+all sparsity paths.
 
 'disable'::
 	Disable the `core.sparseCheckout` config setting, and restore the
-	working directory to include all files. Leaves the sparse-checkout
-	file intact so a later 'git sparse-checkout init' command may
-	return the working directory to the same state.
+	working directory to include all files.
+
+'init'::
+	Deprecated command that behaves like `set` with no specified paths.
+	May be removed in the future.
++
+Historically, `set` did not used to handle all the necessary config
+settings, which meant that both `init` and `set` had to be called.
+Invoking both meant the `init` step would first remove nearly all
+tracked files (and in cone mode, ignored files too), then the `set`
+step would add many of the tracked files (but not ignored files) back.
+In addition to the lost files, the performance and UI of this
+combination was poor.
++
+Also, historically, `init` would not actually initialize the
+sparse-checkout file if it already existed.  This meant it was
+possible to return to a sparse-checkout without remembering which
+paths to pass to a subsequent 'set' or 'add' command.  However,
+`--cone` and `--sparse-index` options would not be remembered across
+the disable command, so the easy restore of calling a plain `init`
+decreased in utility.
 
 SPARSE CHECKOUT
 ---------------
@@ -117,10 +131,8 @@ directory, it updates the skip-worktree bits in the index based
 on this file. The files matching the patterns in the file will
 appear in the working directory, and the rest will not.
 
-To enable the sparse-checkout feature, run `git sparse-checkout init` to
-initialize a simple sparse-checkout file and enable the `core.sparseCheckout`
-config setting. Then, run `git sparse-checkout set` to modify the patterns in
-the sparse-checkout file.
+To enable the sparse-checkout feature, run `git sparse-checkout set` to
+set the patterns you want to use.
 
 To repopulate the working directory with all files, use the
 `git sparse-checkout disable` command.

Documentation/git-clone.txt, Documentation/git-sparse-checkout.txt

diff --git a/Documentation/git-clone.txt b/Documentation/git-clone.txt
index 3fe3810f1ce..b348a71fc68 100644
--- a/Documentation/git-clone.txt
+++ b/Documentation/git-clone.txt
@@ -167,10 +167,10 @@ objects from the source repository into a pack in the cloned repository.
 	configuration variables are created.
 
 --sparse::
-	Initialize the sparse-checkout file so the working
-	directory starts with only the files in the root
-	of the repository. The sparse-checkout file can be
-	modified to grow the working directory as needed.
+	Employ a sparse-checkout, with only files in the toplevel
+	directory initially being present.  The
+	linkgit:git-sparse-checkout[1] command can be used to grow the
+	working directory as needed.
 
 --filter=<filter-spec>::
 	Use the partial clone feature and request that the server sends
diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index c7a25e282e7..aca36782cef 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -121,7 +121,7 @@ SPARSE CHECKOUT
 It uses the skip-worktree bit (see linkgit:git-update-index[1]) to tell
 Git whether a file in the working directory is worth looking at. If
 the skip-worktree bit is set, then the file is ignored in the working
-directory. Git will not populate the contents of those files, which
+directory. Git will avoid populating the contents of those files, which
 makes a sparse checkout helpful when working in a repository with many
 files, but only a few are important to the current user.
 

diff --git a/builtin/clone.c b/builtin/clone.c
index fb377b27657..5bed37f8b51 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -633,7 +633,7 @@ static int git_sparse_checkout_init(const char *repo)
 {
 	struct strvec argv = STRVEC_INIT;
 	int result = 0;
-	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "init", NULL);
+	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "set", NULL);
 
 	/*
 	 * We must apply the setting in the current process

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index d0f5c4702be..8612328e5dd 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -525,7 +525,8 @@ static struct sparse_checkout_set_opts {
 } set_opts;
 
 static void add_patterns_from_input(struct pattern_list *pl,
-				    int argc, const char **argv)
+				    int argc, const char **argv,
+				    int use_stdin)
 {
 	int i;
 	if (core_sparse_checkout_cone) {
@@ -535,7 +536,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 		hashmap_init(&pl->parent_hashmap, pl_hashmap_cmp, NULL, 0);
 		pl->use_cone_patterns = 1;
 
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf unquoted = STRBUF_INIT;
 			while (!strbuf_getline(&line, stdin)) {
 				if (line.buf[0] == '"') {
@@ -559,7 +560,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 			}
 		}
 	} else {
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf line = STRBUF_INIT;
 
 			while (!strbuf_getline(&line, stdin)) {
@@ -580,7 +581,8 @@ enum modify_type {
 };
 
 static void add_patterns_cone_mode(int argc, const char **argv,
-				   struct pattern_list *pl)
+				   struct pattern_list *pl,
+				   int use_stdin)
 {
 	struct strbuf buffer = STRBUF_INIT;
 	struct pattern_entry *pe;
@@ -588,7 +590,7 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 	struct pattern_list existing;
 	char *sparse_filename = get_sparse_checkout_filename();
 
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 
 	memset(&existing, 0, sizeof(existing));
 	existing.use_cone_patterns = core_sparse_checkout_cone;
@@ -614,17 +616,19 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 }
 
 static void add_patterns_literal(int argc, const char **argv,
-				 struct pattern_list *pl)
+				 struct pattern_list *pl,
+				 int use_stdin)
 {
 	char *sparse_filename = get_sparse_checkout_filename();
 	if (add_patterns_from_file_to_list(sparse_filename, "", 0,
 					   pl, NULL, 0))
 		die(_("unable to load existing sparse-checkout patterns"));
 	free(sparse_filename);
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 }
 
-static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
+static int modify_pattern_list(int argc, const char **argv, int use_stdin,
+			       enum modify_type m)
 {
 	int result;
 	int changed_config = 0;
@@ -633,13 +637,13 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 	switch (m) {
 	case ADD:
 		if (core_sparse_checkout_cone)
-			add_patterns_cone_mode(argc, argv, pl);
+			add_patterns_cone_mode(argc, argv, pl, use_stdin);
 		else
-			add_patterns_literal(argc, argv, pl);
+			add_patterns_literal(argc, argv, pl, use_stdin);
 		break;
 
 	case REPLACE:
-		add_patterns_from_input(pl, argc, argv);
+		add_patterns_from_input(pl, argc, argv, use_stdin);
 		break;
 	}
 
@@ -675,7 +679,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 8612328e5dd..e252b82136e 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -515,15 +515,6 @@ static void strbuf_to_cone_pattern(struct strbuf *line, struct pattern_list *pl)
 	insert_recursive_pattern(pl, line);
 }
 
-static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout (set|add) (--stdin | <patterns>)"),
-	NULL
-};
-
-static struct sparse_checkout_set_opts {
-	int use_stdin;
-} set_opts;
-
 static void add_patterns_from_input(struct pattern_list *pl,
 				    int argc, const char **argv,
 				    int use_stdin)
@@ -663,8 +654,43 @@ static int modify_pattern_list(int argc, const char **argv, int use_stdin,
 	return result;
 }
 
-static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
-			       enum modify_type m)
+static char const * const builtin_sparse_checkout_add_usage[] = {
+	N_("git sparse-checkout add (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_add_opts {
+	int use_stdin;
+} add_opts;
+
+static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
+{
+	static struct option builtin_sparse_checkout_add_options[] = {
+		OPT_BOOL(0, "stdin", &add_opts.use_stdin,
+			 N_("read patterns from standard in")),
+		OPT_END(),
+	};
+
+	repo_read_index(the_repository);
+
+	argc = parse_options(argc, argv, prefix,
+			     builtin_sparse_checkout_add_options,
+			     builtin_sparse_checkout_add_usage,
+			     PARSE_OPT_KEEP_UNKNOWN);
+
+	return modify_pattern_list(argc, argv, add_opts.use_stdin, ADD);
+}
+
+static char const * const builtin_sparse_checkout_set_usage[] = {
+	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_set_opts {
+	int use_stdin;
+} set_opts;
+
+static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
 	static struct option builtin_sparse_checkout_set_options[] = {
 		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
@@ -679,7 +705,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {
@@ -762,9 +788,9 @@ int cmd_sparse_checkout(int argc, const char **argv, const char *prefix)
 		if (!strcmp(argv[0], "init"))
 			return sparse_checkout_init(argc, argv);
 		if (!strcmp(argv[0], "set"))
-			return sparse_checkout_set(argc, argv, prefix, REPLACE);
+			return sparse_checkout_set(argc, argv, prefix);
 		if (!strcmp(argv[0], "add"))
-			return sparse_checkout_set(argc, argv, prefix, ADD);
+			return sparse_checkout_add(argc, argv, prefix);
 		if (!strcmp(argv[0], "reapply"))
 			return sparse_checkout_reapply(argc, argv);
 		if (!strcmp(argv[0], "disable"))

builtin/sparse-checkout.c, t/t1091-sparse-checkout-builtin.sh

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index e252b82136e..e9f644ac362 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -56,6 +56,9 @@ static int sparse_checkout_list(int argc, const char **argv)
 	char *sparse_filename;
 	int res;
 
+	if (!core_apply_sparse_checkout)
+		die(_("this worktree is not sparse"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_list_options,
 			     builtin_sparse_checkout_list_usage, 0);
@@ -671,6 +674,9 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 		OPT_END(),
 	};
 
+	if (!core_apply_sparse_checkout)
+		die(_("no sparse-checkout to add to"));
+
 	repo_read_index(the_repository);
 
 	argc = parse_options(argc, argv, prefix,
@@ -719,6 +725,9 @@ static int sparse_checkout_reapply(int argc, const char **argv)
 		OPT_END(),
 	};
 
+	if (!core_apply_sparse_checkout)
+		die(_("must be in a sparse-checkout to reapply sparsity patterns"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_reapply_options,
 			     builtin_sparse_checkout_reapply_usage, 0);
@@ -740,6 +749,9 @@ static int sparse_checkout_disable(int argc, const char **argv)
 	struct pattern_list pl;
 	struct strbuf match_all = STRBUF_INIT;
 
+	if (!core_apply_sparse_checkout)
+		die(_("no active sparse-checkout to disable"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_disable_options,
 			     builtin_sparse_checkout_disable_usage, 0);
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 272ba1b566b..90a281bcf64 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -41,7 +41,15 @@ test_expect_success 'setup' '
 	)
 '
 
-test_expect_success 'git sparse-checkout list (empty)' '
+test_expect_success 'git sparse-checkout list (not sparse)' '
+	test_must_fail git -C repo sparse-checkout list >list 2>err &&
+	test_must_be_empty list &&
+	test_i18ngrep "this worktree is not sparse" err
+'
+
+test_expect_success 'git sparse-checkout list (not sparse)' '
+	git -C repo sparse-checkout set &&
+	rm repo/.git/info/sparse-checkout &&
 	git -C repo sparse-checkout list >list 2>err &&
 	test_must_be_empty list &&
 	test_i18ngrep "this worktree is not sparse (sparse-checkout file may not exist)" err

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index e9f644ac362..0ee28f48134 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -699,8 +699,9 @@ static struct sparse_checkout_set_opts {
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
 	static struct option builtin_sparse_checkout_set_options[] = {
-		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
-			 N_("read patterns from standard in")),
+		OPT_BOOL_F(0, "stdin", &set_opts.use_stdin,
+			   N_("read patterns from standard in"),
+			   PARSE_OPT_NONEG),
 		OPT_END(),
 	};
 

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index f176435b6be..1ecdc3ddd5a 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -706,17 +706,26 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 }
 
 static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	N_("git sparse-checkout set [--[no-]cone] [--[no-]sparse-index] (--stdin | <patterns>)"),
 	NULL
 };
 
 static struct sparse_checkout_set_opts {
+	int cone_mode;
+	int sparse_index;
 	int use_stdin;
 } set_opts;
 
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
+	int default_patterns_nr = 2;
+	const char *default_patterns[] = {"/*", "!/*/", NULL};
+
 	static struct option builtin_sparse_checkout_set_options[] = {
+		OPT_BOOL(0, "cone", &set_opts.cone_mode,
+			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &set_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_BOOL_F(0, "stdin", &set_opts.use_stdin,
 			   N_("read patterns from standard in"),
 			   PARSE_OPT_NONEG),
@@ -725,11 +734,27 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 
 	repo_read_index(the_repository);
 
+	set_opts.cone_mode = -1;
+	set_opts.sparse_index = -1;
+
 	argc = parse_options(argc, argv, prefix,
 			     builtin_sparse_checkout_set_options,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
+	if (update_modes(&set_opts.cone_mode, &set_opts.sparse_index))
+		return 1;
+
+	/*
+	 * Cone mode automatically specifies the toplevel directory.  For
+	 * non-cone mode, if nothing is specified, manually select just the
+	 * top-level directory (much as 'init' would do).
+	 */
+	if (!core_sparse_checkout_cone && argc == 0) {
+		argv = default_patterns;
+		argc = default_patterns_nr;
+	}
+
 	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 0ee28f48134..f176435b6be 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -383,6 +383,41 @@ static int set_config(enum sparse_checkout_mode mode)
 	return 0;
 }
 
+static int update_modes(int *cone_mode, int *sparse_index)
+{
+	int mode, record_mode;
+
+	/* Determine if we need to record the mode; ensure sparse checkout on */
+	record_mode = (*cone_mode != -1) || !core_apply_sparse_checkout;
+
+	/* If not specified, use previous definition of cone mode */
+	if (*cone_mode == -1 && core_apply_sparse_checkout)
+		*cone_mode = core_sparse_checkout_cone;
+
+	/* Set cone/non-cone mode appropriately */
+	core_apply_sparse_checkout = 1;
+	if (*cone_mode == 1) {
+		mode = MODE_CONE_PATTERNS;
+		core_sparse_checkout_cone = 1;
+	} else {
+		mode = MODE_ALL_PATTERNS;
+	}
+	if (record_mode && set_config(mode))
+		return 1;
+
+	/* Set sparse-index/non-sparse-index mode if specified */
+	if (*sparse_index >= 0) {
+		if (set_sparse_index_config(the_repository, *sparse_index) < 0)
+			die(_("failed to modify sparse-index config"));
+
+		/* force an index rewrite */
+		repo_read_index(the_repository);
+		the_repository->index->updated_workdir = 1;
+	}
+
+	return 0;
+}
+
 static char const * const builtin_sparse_checkout_init_usage[] = {
 	N_("git sparse-checkout init [--cone] [--[no-]sparse-index]"),
 	NULL
@@ -399,7 +434,6 @@ static int sparse_checkout_init(int argc, const char **argv)
 	char *sparse_filename;
 	int res;
 	struct object_id oid;
-	int mode;
 	struct strbuf pattern = STRBUF_INIT;
 
 	static struct option builtin_sparse_checkout_init_options[] = {
@@ -412,19 +446,14 @@ static int sparse_checkout_init(int argc, const char **argv)
 
 	repo_read_index(the_repository);
 
+	init_opts.cone_mode = -1;
 	init_opts.sparse_index = -1;
 
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_init_options,
 			     builtin_sparse_checkout_init_usage, 0);
 
-	if (init_opts.cone_mode) {
-		mode = MODE_CONE_PATTERNS;
-		core_sparse_checkout_cone = 1;
-	} else
-		mode = MODE_ALL_PATTERNS;
-
-	if (set_config(mode))
+	if (update_modes(&init_opts.cone_mode, &init_opts.sparse_index))
 		return 1;
 
 	memset(&pl, 0, sizeof(pl));
@@ -432,17 +461,6 @@ static int sparse_checkout_init(int argc, const char **argv)
 	sparse_filename = get_sparse_checkout_filename();
 	res = add_patterns_from_file_to_list(sparse_filename, "", 0, &pl, NULL, 0);
 
-	if (init_opts.sparse_index >= 0) {
-		if (set_sparse_index_config(the_repository, init_opts.sparse_index) < 0)
-			die(_("failed to modify sparse-index config"));
-
-		/* force an index rewrite */
-		repo_read_index(the_repository);
-		the_repository->index->updated_workdir = 1;
-	}
-
-	core_apply_sparse_checkout = 1;
-
 	/* If we already have a sparse-checkout file, use it. */
 	if (res >= 0) {
 		free(sparse_filename);

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 1ecdc3ddd5a..9d2a05677c4 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -759,13 +759,22 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {
-	N_("git sparse-checkout reapply"),
+	N_("git sparse-checkout reapply [--[no-]cone] [--[no-]sparse-index] "),
 	NULL
 };
 
+static struct sparse_checkout_reapply_opts {
+	int cone_mode;
+	int sparse_index;
+} reapply_opts;
+
 static int sparse_checkout_reapply(int argc, const char **argv)
 {
 	static struct option builtin_sparse_checkout_reapply_options[] = {
+		OPT_BOOL(0, "cone", &reapply_opts.cone_mode,
+			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &reapply_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_END(),
 	};
 
@@ -777,6 +786,13 @@ static int sparse_checkout_reapply(int argc, const char **argv)
 			     builtin_sparse_checkout_reapply_usage, 0);
 
 	repo_read_index(the_repository);
+
+	reapply_opts.cone_mode = -1;
+	reapply_opts.sparse_index = -1;
+
+	if (update_modes(&reapply_opts.cone_mode, &reapply_opts.sparse_index))
+		return 1;
+
 	return update_working_directory(NULL);
 }
 

diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index 42056ee9ff9..72fcb6b2acc 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -30,28 +30,36 @@ COMMANDS
 'list'::
 	Describe the patterns in the sparse-checkout file.
 
-'init'::
-	Enable the `core.sparseCheckout` setting. If the
-	sparse-checkout file does not exist, then populate it with
-	patterns that match every file in the root directory and
-	no other directories, then will remove all directories tracked
-	by Git. Add patterns to the sparse-checkout file to
-	repopulate the working directory.
+'set'::
+	Enable the necessary config settings
+	(extensions.worktreeConfig, core.sparseCheckout,
+	core.sparseCheckoutCone) if they are not already enabled, and
+	write a set of patterns to the sparse-checkout file from the
+	list of arguments following the 'set' subcommand. Update the
+	working directory to match the new patterns.
 +
-To avoid interfering with other worktrees, it first enables the
-`extensions.worktreeConfig` setting and makes sure to set the
-`core.sparseCheckout` setting in the worktree-specific config file.
+When the `--stdin` option is provided, the patterns are read from
+standard in as a newline-delimited list instead of from the arguments.
 +
-When `--cone` is provided, the `core.sparseCheckoutCone` setting is
-also set, allowing for better performance with a limited set of
-patterns (see 'CONE PATTERN SET' below).
+When `--cone` is passed or `core.sparseCheckoutCone` is enabled, the
+input list is considered a list of directories instead of
+sparse-checkout patterns.  This allows for better performance with a
+limited set of patterns (see 'CONE PATTERN SET' below).  Note that the
+set command will write patterns to the sparse-checkout file to include
+all files contained in those directories (recursively) as well as
+files that are siblings of ancestor directories. The input format
+matches the output of `git ls-tree --name-only`.  This includes
+interpreting pathnames that begin with a double quote (") as C-style
+quoted strings.  This may become the default in the future; --no-cone
+can be passed to request non-cone mode.
 +
-Use the `--[no-]sparse-index` option to toggle the use of the sparse
-index format. This reduces the size of the index to be more closely
-aligned with your sparse-checkout definition. This can have significant
-performance advantages for commands such as `git status` or `git add`.
-This feature is still experimental. Some commands might be slower with
-a sparse index until they are properly integrated with the feature.
+Use the `--[no-]sparse-index` option to use a sparse index (the
+default is to not use it).  A sparse index reduces the size of the
+index to be more closely aligned with your sparse-checkout
+definition. This can have significant performance advantages for
+commands such as `git status` or `git add`.  This feature is still
+experimental. Some commands might be slower with a sparse index until
+they are properly integrated with the feature.
 +
 **WARNING:** Using a sparse index requires modifying the index in a way
 that is not completely understood by external tools. If you have trouble
@@ -60,23 +68,6 @@ to rewrite your index to not be sparse. Older versions of Git will not
 understand the sparse directory entries index extension and may fail to
 interact with your repository until it is disabled.
 
-'set'::
-	Write a set of patterns to the sparse-checkout file, as given as
-	a list of arguments following the 'set' subcommand. Update the
-	working directory to match the new patterns. Enable the
-	core.sparseCheckout config setting if it is not already enabled.
-+
-When the `--stdin` option is provided, the patterns are read from
-standard in as a newline-delimited list instead of from the arguments.
-+
-When `core.sparseCheckoutCone` is enabled, the input list is considered a
-list of directories instead of sparse-checkout patterns. The command writes
-patterns to the sparse-checkout file to include all files contained in those
-directories (recursively) as well as files that are siblings of ancestor
-directories. The input format matches the output of `git ls-tree --name-only`.
-This includes interpreting pathnames that begin with a double quote (") as
-C-style quoted strings.
-
 'add'::
 	Update the sparse-checkout file to include additional patterns.
 	By default, these patterns are read from the command-line arguments,
@@ -93,12 +84,35 @@ C-style quoted strings.
 	cases, it can make sense to run `git sparse-checkout reapply` later
 	after cleaning up affected paths (e.g. resolving conflicts, undoing
 	or committing changes, etc.).
++
+The `reapply` command can also take `--[no-]cone` and `--[no-]sparse-index`
+flags, with the same meaning as the flags from the `set` command, in order
+to change which sparsity mode you are using without needing to also respecify
+all sparsity paths.
 
 'disable'::
 	Disable the `core.sparseCheckout` config setting, and restore the
-	working directory to include all files. Leaves the sparse-checkout
-	file intact so a later 'git sparse-checkout init' command may
-	return the working directory to the same state.
+	working directory to include all files.
+
+'init'::
+	Deprecated command that behaves like `set` with no specified paths.
+	May be removed in the future.
++
+Historically, `set` did not handle all the necessary config settings,
+which meant that both `init` and `set` had to be called.  Invoking
+both meant the `init` step would first remove nearly all tracked files
+(and in cone mode, ignored files too), then the `set` step would add
+many of the tracked files (but not ignored files) back.  In addition
+to the lost files, the performance and UI of this combination was
+poor.
++
+Also, historically, `init` would not actually initialize the
+sparse-checkout file if it already existed.  This meant it was
+possible to return to a sparse-checkout without remembering which
+paths to pass to a subsequent 'set' or 'add' command.  However,
+`--cone` and `--sparse-index` options would not be remembered across
+the disable command, so the easy restore of calling a plain `init`
+decreased in utility.
 
 SPARSE CHECKOUT
 ---------------
@@ -117,10 +131,8 @@ directory, it updates the skip-worktree bits in the index based
 on this file. The files matching the patterns in the file will
 appear in the working directory, and the rest will not.
 
-To enable the sparse-checkout feature, run `git sparse-checkout init` to
-initialize a simple sparse-checkout file and enable the `core.sparseCheckout`
-config setting. Then, run `git sparse-checkout set` to modify the patterns in
-the sparse-checkout file.
+To enable the sparse-checkout feature, run `git sparse-checkout set` to
+set the patterns you want to use.
 
 To repopulate the working directory with all files, use the
 `git sparse-checkout disable` command.

Documentation/git-clone.txt, Documentation/git-sparse-checkout.txt

diff --git a/Documentation/git-clone.txt b/Documentation/git-clone.txt
index 3fe3810f1ce..b348a71fc68 100644
--- a/Documentation/git-clone.txt
+++ b/Documentation/git-clone.txt
@@ -167,10 +167,10 @@ objects from the source repository into a pack in the cloned repository.
 	configuration variables are created.
 
 --sparse::
-	Initialize the sparse-checkout file so the working
-	directory starts with only the files in the root
-	of the repository. The sparse-checkout file can be
-	modified to grow the working directory as needed.
+	Employ a sparse-checkout, with only files in the toplevel
+	directory initially being present.  The
+	linkgit:git-sparse-checkout[1] command can be used to grow the
+	working directory as needed.
 
 --filter=<filter-spec>::
 	Use the partial clone feature and request that the server sends
diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index 72fcb6b2acc..9a4b43c105b 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -121,7 +121,7 @@ SPARSE CHECKOUT
 It uses the skip-worktree bit (see linkgit:git-update-index[1]) to tell
 Git whether a file in the working directory is worth looking at. If
 the skip-worktree bit is set, then the file is ignored in the working
-directory. Git will not populate the contents of those files, which
+directory. Git will avoid populating the contents of those files, which
 makes a sparse checkout helpful when working in a repository with many
 files, but only a few are important to the current user.
 

diff --git a/builtin/clone.c b/builtin/clone.c
index fb377b27657..5bed37f8b51 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -633,7 +633,7 @@ static int git_sparse_checkout_init(const char *repo)
 {
 	struct strvec argv = STRVEC_INIT;
 	int result = 0;
-	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "init", NULL);
+	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "set", NULL);
 
 	/*
 	 * We must apply the setting in the current process

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index d0f5c4702be..8612328e5dd 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -525,7 +525,8 @@ static struct sparse_checkout_set_opts {
 } set_opts;
 
 static void add_patterns_from_input(struct pattern_list *pl,
-				    int argc, const char **argv)
+				    int argc, const char **argv,
+				    int use_stdin)
 {
 	int i;
 	if (core_sparse_checkout_cone) {
@@ -535,7 +536,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 		hashmap_init(&pl->parent_hashmap, pl_hashmap_cmp, NULL, 0);
 		pl->use_cone_patterns = 1;
 
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf unquoted = STRBUF_INIT;
 			while (!strbuf_getline(&line, stdin)) {
 				if (line.buf[0] == '"') {
@@ -559,7 +560,7 @@ static void add_patterns_from_input(struct pattern_list *pl,
 			}
 		}
 	} else {
-		if (set_opts.use_stdin) {
+		if (use_stdin) {
 			struct strbuf line = STRBUF_INIT;
 
 			while (!strbuf_getline(&line, stdin)) {
@@ -580,7 +581,8 @@ enum modify_type {
 };
 
 static void add_patterns_cone_mode(int argc, const char **argv,
-				   struct pattern_list *pl)
+				   struct pattern_list *pl,
+				   int use_stdin)
 {
 	struct strbuf buffer = STRBUF_INIT;
 	struct pattern_entry *pe;
@@ -588,7 +590,7 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 	struct pattern_list existing;
 	char *sparse_filename = get_sparse_checkout_filename();
 
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 
 	memset(&existing, 0, sizeof(existing));
 	existing.use_cone_patterns = core_sparse_checkout_cone;
@@ -614,17 +616,19 @@ static void add_patterns_cone_mode(int argc, const char **argv,
 }
 
 static void add_patterns_literal(int argc, const char **argv,
-				 struct pattern_list *pl)
+				 struct pattern_list *pl,
+				 int use_stdin)
 {
 	char *sparse_filename = get_sparse_checkout_filename();
 	if (add_patterns_from_file_to_list(sparse_filename, "", 0,
 					   pl, NULL, 0))
 		die(_("unable to load existing sparse-checkout patterns"));
 	free(sparse_filename);
-	add_patterns_from_input(pl, argc, argv);
+	add_patterns_from_input(pl, argc, argv, use_stdin);
 }
 
-static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
+static int modify_pattern_list(int argc, const char **argv, int use_stdin,
+			       enum modify_type m)
 {
 	int result;
 	int changed_config = 0;
@@ -633,13 +637,13 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 	switch (m) {
 	case ADD:
 		if (core_sparse_checkout_cone)
-			add_patterns_cone_mode(argc, argv, pl);
+			add_patterns_cone_mode(argc, argv, pl, use_stdin);
 		else
-			add_patterns_literal(argc, argv, pl);
+			add_patterns_literal(argc, argv, pl, use_stdin);
 		break;
 
 	case REPLACE:
-		add_patterns_from_input(pl, argc, argv);
+		add_patterns_from_input(pl, argc, argv, use_stdin);
 		break;
 	}
 
@@ -675,7 +679,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 8612328e5dd..e252b82136e 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -515,15 +515,6 @@ static void strbuf_to_cone_pattern(struct strbuf *line, struct pattern_list *pl)
 	insert_recursive_pattern(pl, line);
 }
 
-static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout (set|add) (--stdin | <patterns>)"),
-	NULL
-};
-
-static struct sparse_checkout_set_opts {
-	int use_stdin;
-} set_opts;
-
 static void add_patterns_from_input(struct pattern_list *pl,
 				    int argc, const char **argv,
 				    int use_stdin)
@@ -663,8 +654,43 @@ static int modify_pattern_list(int argc, const char **argv, int use_stdin,
 	return result;
 }
 
-static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
-			       enum modify_type m)
+static char const * const builtin_sparse_checkout_add_usage[] = {
+	N_("git sparse-checkout add (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_add_opts {
+	int use_stdin;
+} add_opts;
+
+static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
+{
+	static struct option builtin_sparse_checkout_add_options[] = {
+		OPT_BOOL(0, "stdin", &add_opts.use_stdin,
+			 N_("read patterns from standard in")),
+		OPT_END(),
+	};
+
+	repo_read_index(the_repository);
+
+	argc = parse_options(argc, argv, prefix,
+			     builtin_sparse_checkout_add_options,
+			     builtin_sparse_checkout_add_usage,
+			     PARSE_OPT_KEEP_UNKNOWN);
+
+	return modify_pattern_list(argc, argv, add_opts.use_stdin, ADD);
+}
+
+static char const * const builtin_sparse_checkout_set_usage[] = {
+	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	NULL
+};
+
+static struct sparse_checkout_set_opts {
+	int use_stdin;
+} set_opts;
+
+static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
 	static struct option builtin_sparse_checkout_set_options[] = {
 		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
@@ -679,7 +705,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
-	return modify_pattern_list(argc, argv, set_opts.use_stdin, m);
+	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {
@@ -762,9 +788,9 @@ int cmd_sparse_checkout(int argc, const char **argv, const char *prefix)
 		if (!strcmp(argv[0], "init"))
 			return sparse_checkout_init(argc, argv);
 		if (!strcmp(argv[0], "set"))
-			return sparse_checkout_set(argc, argv, prefix, REPLACE);
+			return sparse_checkout_set(argc, argv, prefix);
 		if (!strcmp(argv[0], "add"))
-			return sparse_checkout_set(argc, argv, prefix, ADD);
+			return sparse_checkout_add(argc, argv, prefix);
 		if (!strcmp(argv[0], "reapply"))
 			return sparse_checkout_reapply(argc, argv);
 		if (!strcmp(argv[0], "disable"))

builtin/sparse-checkout.c, t/t1091-sparse-checkout-builtin.sh

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index e252b82136e..eb8fbd36b0b 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -56,6 +56,9 @@ static int sparse_checkout_list(int argc, const char **argv)
 	char *sparse_filename;
 	int res;
 
+	if (!core_apply_sparse_checkout)
+		die(_("this worktree is not sparse"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_list_options,
 			     builtin_sparse_checkout_list_usage, 0);
@@ -671,6 +674,9 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 		OPT_END(),
 	};
 
+	if (!core_apply_sparse_checkout)
+		die(_("no sparse-checkout to add to"));
+
 	repo_read_index(the_repository);
 
 	argc = parse_options(argc, argv, prefix,
@@ -719,6 +725,9 @@ static int sparse_checkout_reapply(int argc, const char **argv)
 		OPT_END(),
 	};
 
+	if (!core_apply_sparse_checkout)
+		die(_("must be in a sparse-checkout to reapply sparsity patterns"));
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_reapply_options,
 			     builtin_sparse_checkout_reapply_usage, 0);
@@ -740,6 +749,17 @@ static int sparse_checkout_disable(int argc, const char **argv)
 	struct pattern_list pl;
 	struct strbuf match_all = STRBUF_INIT;
 
+	/*
+	 * We do not exit early if !core_apply_sparse_checkout; due to the
+	 * ability for users to manually muck things up between
+	 *   direct editing of .git/info/sparse-checkout
+	 *   running read-tree -m u HEAD or update-index --skip-worktree
+	 *   direct toggling of config options
+	 * users might end up with an index with SKIP_WORKTREE bit set on
+	 * some files and not know how to undo it.  So, here we just
+	 * forcibly return to a dense checkout regardless of initial state.
+	 */
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_disable_options,
 			     builtin_sparse_checkout_disable_usage, 0);
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 272ba1b566b..90a281bcf64 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -41,7 +41,15 @@ test_expect_success 'setup' '
 	)
 '
 
-test_expect_success 'git sparse-checkout list (empty)' '
+test_expect_success 'git sparse-checkout list (not sparse)' '
+	test_must_fail git -C repo sparse-checkout list >list 2>err &&
+	test_must_be_empty list &&
+	test_i18ngrep "this worktree is not sparse" err
+'
+
+test_expect_success 'git sparse-checkout list (not sparse)' '
+	git -C repo sparse-checkout set &&
+	rm repo/.git/info/sparse-checkout &&
 	git -C repo sparse-checkout list >list 2>err &&
 	test_must_be_empty list &&
 	test_i18ngrep "this worktree is not sparse (sparse-checkout file may not exist)" err

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index eb8fbd36b0b..387903eafe7 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -699,8 +699,9 @@ static struct sparse_checkout_set_opts {
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
 	static struct option builtin_sparse_checkout_set_options[] = {
-		OPT_BOOL(0, "stdin", &set_opts.use_stdin,
-			 N_("read patterns from standard in")),
+		OPT_BOOL_F(0, "stdin", &set_opts.use_stdin,
+			   N_("read patterns from standard in"),
+			   PARSE_OPT_NONEG),
 		OPT_END(),
 	};
 

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 387903eafe7..3b74779bb48 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -383,6 +383,41 @@ static int set_config(enum sparse_checkout_mode mode)
 	return 0;
 }
 
+static int update_modes(int *cone_mode, int *sparse_index)
+{
+	int mode, record_mode;
+
+	/* Determine if we need to record the mode; ensure sparse checkout on */
+	record_mode = (*cone_mode != -1) || !core_apply_sparse_checkout;
+
+	/* If not specified, use previous definition of cone mode */
+	if (*cone_mode == -1 && core_apply_sparse_checkout)
+		*cone_mode = core_sparse_checkout_cone;
+
+	/* Set cone/non-cone mode appropriately */
+	core_apply_sparse_checkout = 1;
+	if (*cone_mode == 1) {
+		mode = MODE_CONE_PATTERNS;
+		core_sparse_checkout_cone = 1;
+	} else {
+		mode = MODE_ALL_PATTERNS;
+	}
+	if (record_mode && set_config(mode))
+		return 1;
+
+	/* Set sparse-index/non-sparse-index mode if specified */
+	if (*sparse_index >= 0) {
+		if (set_sparse_index_config(the_repository, *sparse_index) < 0)
+			die(_("failed to modify sparse-index config"));
+
+		/* force an index rewrite */
+		repo_read_index(the_repository);
+		the_repository->index->updated_workdir = 1;
+	}
+
+	return 0;
+}
+
 static char const * const builtin_sparse_checkout_init_usage[] = {
 	N_("git sparse-checkout init [--cone] [--[no-]sparse-index]"),
 	NULL
@@ -399,7 +434,6 @@ static int sparse_checkout_init(int argc, const char **argv)
 	char *sparse_filename;
 	int res;
 	struct object_id oid;
-	int mode;
 	struct strbuf pattern = STRBUF_INIT;
 
 	static struct option builtin_sparse_checkout_init_options[] = {
@@ -412,19 +446,14 @@ static int sparse_checkout_init(int argc, const char **argv)
 
 	repo_read_index(the_repository);
 
+	init_opts.cone_mode = -1;
 	init_opts.sparse_index = -1;
 
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_init_options,
 			     builtin_sparse_checkout_init_usage, 0);
 
-	if (init_opts.cone_mode) {
-		mode = MODE_CONE_PATTERNS;
-		core_sparse_checkout_cone = 1;
-	} else
-		mode = MODE_ALL_PATTERNS;
-
-	if (set_config(mode))
+	if (update_modes(&init_opts.cone_mode, &init_opts.sparse_index))
 		return 1;
 
 	memset(&pl, 0, sizeof(pl));
@@ -432,17 +461,6 @@ static int sparse_checkout_init(int argc, const char **argv)
 	sparse_filename = get_sparse_checkout_filename();
 	res = add_patterns_from_file_to_list(sparse_filename, "", 0, &pl, NULL, 0);
 
-	if (init_opts.sparse_index >= 0) {
-		if (set_sparse_index_config(the_repository, init_opts.sparse_index) < 0)
-			die(_("failed to modify sparse-index config"));
-
-		/* force an index rewrite */
-		repo_read_index(the_repository);
-		the_repository->index->updated_workdir = 1;
-	}
-
-	core_apply_sparse_checkout = 1;
-
 	/* If we already have a sparse-checkout file, use it. */
 	if (res >= 0) {
 		free(sparse_filename);

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 16daae84975..0dae44c5759 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -759,13 +759,22 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 }
 
 static char const * const builtin_sparse_checkout_reapply_usage[] = {
-	N_("git sparse-checkout reapply"),
+	N_("git sparse-checkout reapply [--[no-]cone] [--[no-]sparse-index] "),
 	NULL
 };
 
+static struct sparse_checkout_reapply_opts {
+	int cone_mode;
+	int sparse_index;
+} reapply_opts;
+
 static int sparse_checkout_reapply(int argc, const char **argv)
 {
 	static struct option builtin_sparse_checkout_reapply_options[] = {
+		OPT_BOOL(0, "cone", &reapply_opts.cone_mode,
+			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &reapply_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_END(),
 	};
 
@@ -777,6 +786,13 @@ static int sparse_checkout_reapply(int argc, const char **argv)
 			     builtin_sparse_checkout_reapply_usage, 0);
 
 	repo_read_index(the_repository);
+
+	reapply_opts.cone_mode = -1;
+	reapply_opts.sparse_index = -1;
+
+	if (update_modes(&reapply_opts.cone_mode, &reapply_opts.sparse_index))
+		return 1;
+
 	return update_working_directory(NULL);
 }
 

Documentation/git-clone.txt, Documentation/git-sparse-checkout.txt

diff --git a/Documentation/git-clone.txt b/Documentation/git-clone.txt
index 3fe3810f1ce..b348a71fc68 100644
--- a/Documentation/git-clone.txt
+++ b/Documentation/git-clone.txt
@@ -167,10 +167,10 @@ objects from the source repository into a pack in the cloned repository.
 	configuration variables are created.
 
 --sparse::
-	Initialize the sparse-checkout file so the working
-	directory starts with only the files in the root
-	of the repository. The sparse-checkout file can be
-	modified to grow the working directory as needed.
+	Employ a sparse-checkout, with only files in the toplevel
+	directory initially being present.  The
+	linkgit:git-sparse-checkout[1] command can be used to grow the
+	working directory as needed.
 
 --filter=<filter-spec>::
 	Use the partial clone feature and request that the server sends
diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index 72fcb6b2acc..9a4b43c105b 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -121,7 +121,7 @@ SPARSE CHECKOUT
 It uses the skip-worktree bit (see linkgit:git-update-index[1]) to tell
 Git whether a file in the working directory is worth looking at. If
 the skip-worktree bit is set, then the file is ignored in the working
-directory. Git will not populate the contents of those files, which
+directory. Git will avoid populating the contents of those files, which
 makes a sparse checkout helpful when working in a repository with many
 files, but only a few are important to the current user.
 

diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index 42056ee9ff9..72fcb6b2acc 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -30,28 +30,36 @@ COMMANDS
 'list'::
 	Describe the patterns in the sparse-checkout file.
 
-'init'::
-	Enable the `core.sparseCheckout` setting. If the
-	sparse-checkout file does not exist, then populate it with
-	patterns that match every file in the root directory and
-	no other directories, then will remove all directories tracked
-	by Git. Add patterns to the sparse-checkout file to
-	repopulate the working directory.
+'set'::
+	Enable the necessary config settings
+	(extensions.worktreeConfig, core.sparseCheckout,
+	core.sparseCheckoutCone) if they are not already enabled, and
+	write a set of patterns to the sparse-checkout file from the
+	list of arguments following the 'set' subcommand. Update the
+	working directory to match the new patterns.
 +
-To avoid interfering with other worktrees, it first enables the
-`extensions.worktreeConfig` setting and makes sure to set the
-`core.sparseCheckout` setting in the worktree-specific config file.
+When the `--stdin` option is provided, the patterns are read from
+standard in as a newline-delimited list instead of from the arguments.
 +
-When `--cone` is provided, the `core.sparseCheckoutCone` setting is
-also set, allowing for better performance with a limited set of
-patterns (see 'CONE PATTERN SET' below).
+When `--cone` is passed or `core.sparseCheckoutCone` is enabled, the
+input list is considered a list of directories instead of
+sparse-checkout patterns.  This allows for better performance with a
+limited set of patterns (see 'CONE PATTERN SET' below).  Note that the
+set command will write patterns to the sparse-checkout file to include
+all files contained in those directories (recursively) as well as
+files that are siblings of ancestor directories. The input format
+matches the output of `git ls-tree --name-only`.  This includes
+interpreting pathnames that begin with a double quote (") as C-style
+quoted strings.  This may become the default in the future; --no-cone
+can be passed to request non-cone mode.
 +
-Use the `--[no-]sparse-index` option to toggle the use of the sparse
-index format. This reduces the size of the index to be more closely
-aligned with your sparse-checkout definition. This can have significant
-performance advantages for commands such as `git status` or `git add`.
-This feature is still experimental. Some commands might be slower with
-a sparse index until they are properly integrated with the feature.
+Use the `--[no-]sparse-index` option to use a sparse index (the
+default is to not use it).  A sparse index reduces the size of the
+index to be more closely aligned with your sparse-checkout
+definition. This can have significant performance advantages for
+commands such as `git status` or `git add`.  This feature is still
+experimental. Some commands might be slower with a sparse index until
+they are properly integrated with the feature.
 +
 **WARNING:** Using a sparse index requires modifying the index in a way
 that is not completely understood by external tools. If you have trouble
@@ -60,23 +68,6 @@ to rewrite your index to not be sparse. Older versions of Git will not
 understand the sparse directory entries index extension and may fail to
 interact with your repository until it is disabled.
 
-'set'::
-	Write a set of patterns to the sparse-checkout file, as given as
-	a list of arguments following the 'set' subcommand. Update the
-	working directory to match the new patterns. Enable the
-	core.sparseCheckout config setting if it is not already enabled.
-+
-When the `--stdin` option is provided, the patterns are read from
-standard in as a newline-delimited list instead of from the arguments.
-+
-When `core.sparseCheckoutCone` is enabled, the input list is considered a
-list of directories instead of sparse-checkout patterns. The command writes
-patterns to the sparse-checkout file to include all files contained in those
-directories (recursively) as well as files that are siblings of ancestor
-directories. The input format matches the output of `git ls-tree --name-only`.
-This includes interpreting pathnames that begin with a double quote (") as
-C-style quoted strings.
-
 'add'::
 	Update the sparse-checkout file to include additional patterns.
 	By default, these patterns are read from the command-line arguments,
@@ -93,12 +84,35 @@ C-style quoted strings.
 	cases, it can make sense to run `git sparse-checkout reapply` later
 	after cleaning up affected paths (e.g. resolving conflicts, undoing
 	or committing changes, etc.).
++
+The `reapply` command can also take `--[no-]cone` and `--[no-]sparse-index`
+flags, with the same meaning as the flags from the `set` command, in order
+to change which sparsity mode you are using without needing to also respecify
+all sparsity paths.
 
 'disable'::
 	Disable the `core.sparseCheckout` config setting, and restore the
-	working directory to include all files. Leaves the sparse-checkout
-	file intact so a later 'git sparse-checkout init' command may
-	return the working directory to the same state.
+	working directory to include all files.
+
+'init'::
+	Deprecated command that behaves like `set` with no specified paths.
+	May be removed in the future.
++
+Historically, `set` did not handle all the necessary config settings,
+which meant that both `init` and `set` had to be called.  Invoking
+both meant the `init` step would first remove nearly all tracked files
+(and in cone mode, ignored files too), then the `set` step would add
+many of the tracked files (but not ignored files) back.  In addition
+to the lost files, the performance and UI of this combination was
+poor.
++
+Also, historically, `init` would not actually initialize the
+sparse-checkout file if it already existed.  This meant it was
+possible to return to a sparse-checkout without remembering which
+paths to pass to a subsequent 'set' or 'add' command.  However,
+`--cone` and `--sparse-index` options would not be remembered across
+the disable command, so the easy restore of calling a plain `init`
+decreased in utility.
 
 SPARSE CHECKOUT
 ---------------
@@ -117,10 +131,8 @@ directory, it updates the skip-worktree bits in the index based
 on this file. The files matching the patterns in the file will
 appear in the working directory, and the rest will not.
 
-To enable the sparse-checkout feature, run `git sparse-checkout init` to
-initialize a simple sparse-checkout file and enable the `core.sparseCheckout`
-config setting. Then, run `git sparse-checkout set` to modify the patterns in
-the sparse-checkout file.
+To enable the sparse-checkout feature, run `git sparse-checkout set` to
+set the patterns you want to use.
 
 To repopulate the working directory with all files, use the
 `git sparse-checkout disable` command.

diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 3b74779bb48..16daae84975 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -706,17 +706,26 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 }
 
 static char const * const builtin_sparse_checkout_set_usage[] = {
-	N_("git sparse-checkout set (--stdin | <patterns>)"),
+	N_("git sparse-checkout set [--[no-]cone] [--[no-]sparse-index] (--stdin | <patterns>)"),
 	NULL
 };
 
 static struct sparse_checkout_set_opts {
+	int cone_mode;
+	int sparse_index;
 	int use_stdin;
 } set_opts;
 
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 {
+	int default_patterns_nr = 2;
+	const char *default_patterns[] = {"/*", "!/*/", NULL};
+
 	static struct option builtin_sparse_checkout_set_options[] = {
+		OPT_BOOL(0, "cone", &set_opts.cone_mode,
+			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &set_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_BOOL_F(0, "stdin", &set_opts.use_stdin,
 			   N_("read patterns from standard in"),
 			   PARSE_OPT_NONEG),
@@ -725,11 +734,27 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 
 	repo_read_index(the_repository);
 
+	set_opts.cone_mode = -1;
+	set_opts.sparse_index = -1;
+
 	argc = parse_options(argc, argv, prefix,
 			     builtin_sparse_checkout_set_options,
 			     builtin_sparse_checkout_set_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
+	if (update_modes(&set_opts.cone_mode, &set_opts.sparse_index))
+		return 1;
+
+	/*
+	 * Cone mode automatically specifies the toplevel directory.  For
+	 * non-cone mode, if nothing is specified, manually select just the
+	 * top-level directory (much as 'init' would do).
+	 */
+	if (!core_sparse_checkout_cone && argc == 0) {
+		argv = default_patterns;
+		argc = default_patterns_nr;
+	}
+
 	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
 }
 

diff --git a/builtin/clone.c b/builtin/clone.c
index fb377b27657..5bed37f8b51 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -633,7 +633,7 @@ static int git_sparse_checkout_init(const char *repo)
 {
 	struct strvec argv = STRVEC_INIT;
 	int result = 0;
-	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "init", NULL);
+	strvec_pushl(&argv, "-C", repo, "sparse-checkout", "set", NULL);
 
 	/*
 	 * We must apply the setting in the current process