diff --git a/Documentation/git-sparse-checkout.adoc b/Documentation/git-sparse-checkout.adoc
index 529a8edd9c1ed8..604f53f77caf4c 100644
--- a/Documentation/git-sparse-checkout.adoc
+++ b/Documentation/git-sparse-checkout.adoc
@@ -9,7 +9,7 @@ git-sparse-checkout - Reduce your working tree to a subset of tracked files
 SYNOPSIS
 --------
 [verse]
-'git sparse-checkout' (init | list | set | add | reapply | disable | check-rules) [<options>]
+'git sparse-checkout' (init | list | set | add | reapply | disable | check-rules | clean) [<options>]
 
 
 DESCRIPTION
@@ -111,6 +111,29 @@ 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.
 
+'clean'::
+	Remove all files in tracked directories that are outside of the
+	sparse-checkout definition. This subcommand requires cone-mode
+	sparse-checkout to be sure that we know which directories are
+	both tracked and all contained paths are not in the sparse-checkout.
+	This command can be used to be sure the sparse index works
+	efficiently, though it does not require enabling the sparse index
+  feature via the `index.sparse=true` configuration.
++
+To prevent accidental deletion of worktree files, the `clean` subcommand
+will not delete any files without the `-f` or `--force` option, unless
+the `clean.requireForce` config option is set to `false`.
++
+The `--dry-run` option will list the directories that would be removed
+without deleting them. Running in this mode can be helpful to predict the
+behavior of the clean comand or to determine which kinds of files are left
+in the sparse directories.
++
+The `--verbose` option will list every file within the directories that
+are considered for removal. This option is helpful to determine if those
+files are actually important or perhaps to explain why the directory is
+still present despite the current sparse-checkout.
+
 'disable'::
 	Disable the `core.sparseCheckout` config setting, and restore the
 	working directory to include all files.
diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 8a0ffba9d4b3bf..1d1d5208a3ba33 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -2,6 +2,7 @@
 #define DISABLE_SIGN_COMPARE_WARNINGS
 
 #include "builtin.h"
+#include "abspath.h"
 #include "config.h"
 #include "dir.h"
 #include "environment.h"
@@ -23,7 +24,7 @@
 static const char *empty_base = "";
 
 static char const * const builtin_sparse_checkout_usage[] = {
-	N_("git sparse-checkout (init | list | set | add | reapply | disable | check-rules) [<options>]"),
+	N_("git sparse-checkout (init | list | set | add | reapply | disable | check-rules | clean) [<options>]"),
 	NULL
 };
 
@@ -204,12 +205,12 @@ static void clean_tracked_sparse_directories(struct repository *r)
 		ensure_full_index(r->index);
 }
 
-static int update_working_directory(struct pattern_list *pl)
+static int update_working_directory(struct repository *r,
+				    struct pattern_list *pl)
 {
 	enum update_sparsity_result result;
 	struct unpack_trees_options o;
 	struct lock_file lock_file = LOCK_INIT;
-	struct repository *r = the_repository;
 	struct pattern_list *old_pl;
 
 	/* If no branch has been checked out, there are no updates to make. */
@@ -327,7 +328,8 @@ static void write_cone_to_file(FILE *fp, struct pattern_list *pl)
 	string_list_clear(&sl, 0);
 }
 
-static int write_patterns_and_update(struct pattern_list *pl)
+static int write_patterns_and_update(struct repository *repo,
+				     struct pattern_list *pl)
 {
 	char *sparse_filename;
 	FILE *fp;
@@ -336,15 +338,15 @@ static int write_patterns_and_update(struct pattern_list *pl)
 
 	sparse_filename = get_sparse_checkout_filename();
 
-	if (safe_create_leading_directories(the_repository, sparse_filename))
+	if (safe_create_leading_directories(repo, sparse_filename))
 		die(_("failed to create directory for sparse-checkout file"));
 
 	hold_lock_file_for_update(&lk, sparse_filename, LOCK_DIE_ON_ERROR);
 
-	result = update_working_directory(pl);
+	result = update_working_directory(repo, pl);
 	if (result) {
 		rollback_lock_file(&lk);
-		update_working_directory(NULL);
+		update_working_directory(repo, NULL);
 		goto out;
 	}
 
@@ -372,25 +374,26 @@ enum sparse_checkout_mode {
 	MODE_CONE_PATTERNS = 2,
 };
 
-static int set_config(enum sparse_checkout_mode mode)
+static int set_config(struct repository *repo,
+		      enum sparse_checkout_mode mode)
 {
 	/* Update to use worktree config, if not already. */
-	if (init_worktree_config(the_repository)) {
+	if (init_worktree_config(repo)) {
 		error(_("failed to initialize worktree config"));
 		return 1;
 	}
 
-	if (repo_config_set_worktree_gently(the_repository,
+	if (repo_config_set_worktree_gently(repo,
 					    "core.sparseCheckout",
 					    mode ? "true" : "false") ||
-	    repo_config_set_worktree_gently(the_repository,
+	    repo_config_set_worktree_gently(repo,
 					    "core.sparseCheckoutCone",
 					    mode == MODE_CONE_PATTERNS ?
 						"true" : "false"))
 		return 1;
 
 	if (mode == MODE_NO_PATTERNS)
-		return set_sparse_index_config(the_repository, 0);
+		return set_sparse_index_config(repo, 0);
 
 	return 0;
 }
@@ -410,7 +413,7 @@ static enum sparse_checkout_mode update_cone_mode(int *cone_mode) {
 	return MODE_ALL_PATTERNS;
 }
 
-static int update_modes(int *cone_mode, int *sparse_index)
+static int update_modes(struct repository *repo, int *cone_mode, int *sparse_index)
 {
 	int mode, record_mode;
 
@@ -418,20 +421,20 @@ static int update_modes(int *cone_mode, int *sparse_index)
 	record_mode = (*cone_mode != -1) || !the_repository->settings.sparse_checkout;
 
 	mode = update_cone_mode(cone_mode);
-	if (record_mode && set_config(mode))
+	if (record_mode && set_config(repo, 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)
+		if (set_sparse_index_config(repo, *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;
+		repo_read_index(repo);
+		repo->index->updated_workdir = 1;
 
 		if (!*sparse_index)
-			ensure_full_index(the_repository->index);
+			ensure_full_index(repo->index);
 	}
 
 	return 0;
@@ -448,7 +451,7 @@ static struct sparse_checkout_init_opts {
 } init_opts;
 
 static int sparse_checkout_init(int argc, const char **argv, const char *prefix,
-				struct repository *repo UNUSED)
+				struct repository *repo)
 {
 	struct pattern_list pl;
 	char *sparse_filename;
@@ -464,7 +467,7 @@ static int sparse_checkout_init(int argc, const char **argv, const char *prefix,
 	};
 
 	setup_work_tree();
-	repo_read_index(the_repository);
+	repo_read_index(repo);
 
 	init_opts.cone_mode = -1;
 	init_opts.sparse_index = -1;
@@ -473,7 +476,7 @@ static int sparse_checkout_init(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_init_options,
 			     builtin_sparse_checkout_init_usage, 0);
 
-	if (update_modes(&init_opts.cone_mode, &init_opts.sparse_index))
+	if (update_modes(repo, &init_opts.cone_mode, &init_opts.sparse_index))
 		return 1;
 
 	memset(&pl, 0, sizeof(pl));
@@ -485,14 +488,14 @@ static int sparse_checkout_init(int argc, const char **argv, const char *prefix,
 	if (res >= 0) {
 		free(sparse_filename);
 		clear_pattern_list(&pl);
-		return update_working_directory(NULL);
+		return update_working_directory(repo, NULL);
 	}
 
-	if (repo_get_oid(the_repository, "HEAD", &oid)) {
+	if (repo_get_oid(repo, "HEAD", &oid)) {
 		FILE *fp;
 
 		/* assume we are in a fresh repo, but update the sparse-checkout file */
-		if (safe_create_leading_directories(the_repository, sparse_filename))
+		if (safe_create_leading_directories(repo, sparse_filename))
 			die(_("unable to create leading directories of %s"),
 			    sparse_filename);
 		fp = xfopen(sparse_filename, "w");
@@ -511,7 +514,7 @@ static int sparse_checkout_init(int argc, const char **argv, const char *prefix,
 	add_pattern("!/*/", empty_base, 0, &pl, 0);
 	pl.use_cone_patterns = init_opts.cone_mode;
 
-	return write_patterns_and_update(&pl);
+	return write_patterns_and_update(repo, &pl);
 }
 
 static void insert_recursive_pattern(struct pattern_list *pl, struct strbuf *path)
@@ -674,7 +677,8 @@ static void add_patterns_literal(int argc, const char **argv,
 	add_patterns_from_input(pl, argc, argv, use_stdin ? stdin : NULL);
 }
 
-static int modify_pattern_list(struct strvec *args, int use_stdin,
+static int modify_pattern_list(struct repository *repo,
+			       struct strvec *args, int use_stdin,
 			       enum modify_type m)
 {
 	int result;
@@ -695,23 +699,24 @@ static int modify_pattern_list(struct strvec *args, int use_stdin,
 		break;
 	}
 
-	if (!the_repository->settings.sparse_checkout) {
-		set_config(MODE_ALL_PATTERNS);
-		the_repository->settings.sparse_checkout = 1;
+	if (!repo->settings.sparse_checkout) {
+		set_config(repo, MODE_ALL_PATTERNS);
+		repo->settings.sparse_checkout = 1;
 		changed_config = 1;
 	}
 
-	result = write_patterns_and_update(pl);
+	result = write_patterns_and_update(repo, pl);
 
 	if (result && changed_config)
-		set_config(MODE_NO_PATTERNS);
+		set_config(repo, MODE_NO_PATTERNS);
 
 	clear_pattern_list(pl);
 	free(pl);
 	return result;
 }
 
-static void sanitize_paths(struct strvec *args,
+static void sanitize_paths(struct repository *repo,
+			   struct strvec *args,
 			   const char *prefix, int skip_checks)
 {
 	int i;
@@ -752,7 +757,7 @@ static void sanitize_paths(struct strvec *args,
 
 	for (i = 0; i < args->nr; i++) {
 		struct cache_entry *ce;
-		struct index_state *index = the_repository->index;
+		struct index_state *index = repo->index;
 		int pos = index_name_pos(index, args->v[i], strlen(args->v[i]));
 
 		if (pos < 0)
@@ -779,7 +784,7 @@ static struct sparse_checkout_add_opts {
 } add_opts;
 
 static int sparse_checkout_add(int argc, const char **argv, const char *prefix,
-			       struct repository *repo UNUSED)
+			       struct repository *repo)
 {
 	static struct option builtin_sparse_checkout_add_options[] = {
 		OPT_BOOL_F(0, "skip-checks", &add_opts.skip_checks,
@@ -796,7 +801,7 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix,
 	if (!the_repository->settings.sparse_checkout)
 		die(_("no sparse-checkout to add to"));
 
-	repo_read_index(the_repository);
+	repo_read_index(repo);
 
 	argc = parse_options(argc, argv, prefix,
 			     builtin_sparse_checkout_add_options,
@@ -804,9 +809,9 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix,
 
 	for (int i = 0; i < argc; i++)
 		strvec_push(&patterns, argv[i]);
-	sanitize_paths(&patterns, prefix, add_opts.skip_checks);
+	sanitize_paths(repo, &patterns, prefix, add_opts.skip_checks);
 
-	ret = modify_pattern_list(&patterns, add_opts.use_stdin, ADD);
+	ret = modify_pattern_list(repo, &patterns, add_opts.use_stdin, ADD);
 
 	strvec_clear(&patterns);
 	return ret;
@@ -825,7 +830,7 @@ static struct sparse_checkout_set_opts {
 } set_opts;
 
 static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
-			       struct repository *repo UNUSED)
+			       struct repository *repo)
 {
 	int default_patterns_nr = 2;
 	const char *default_patterns[] = {"/*", "!/*/", NULL};
@@ -847,7 +852,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 	int ret;
 
 	setup_work_tree();
-	repo_read_index(the_repository);
+	repo_read_index(repo);
 
 	set_opts.cone_mode = -1;
 	set_opts.sparse_index = -1;
@@ -856,7 +861,7 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 			     builtin_sparse_checkout_set_options,
 			     builtin_sparse_checkout_set_usage, 0);
 
-	if (update_modes(&set_opts.cone_mode, &set_opts.sparse_index))
+	if (update_modes(repo, &set_opts.cone_mode, &set_opts.sparse_index))
 		return 1;
 
 	/*
@@ -870,10 +875,10 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 	} else {
 		for (int i = 0; i < argc; i++)
 			strvec_push(&patterns, argv[i]);
-		sanitize_paths(&patterns, prefix, set_opts.skip_checks);
+		sanitize_paths(repo, &patterns, prefix, set_opts.skip_checks);
 	}
 
-	ret = modify_pattern_list(&patterns, set_opts.use_stdin, REPLACE);
+	ret = modify_pattern_list(repo, &patterns, set_opts.use_stdin, REPLACE);
 
 	strvec_clear(&patterns);
 	return ret;
@@ -891,7 +896,7 @@ static struct sparse_checkout_reapply_opts {
 
 static int sparse_checkout_reapply(int argc, const char **argv,
 				   const char *prefix,
-				   struct repository *repo UNUSED)
+				   struct repository *repo)
 {
 	static struct option builtin_sparse_checkout_reapply_options[] = {
 		OPT_BOOL(0, "cone", &reapply_opts.cone_mode,
@@ -912,12 +917,117 @@ static int sparse_checkout_reapply(int argc, const char **argv,
 			     builtin_sparse_checkout_reapply_options,
 			     builtin_sparse_checkout_reapply_usage, 0);
 
-	repo_read_index(the_repository);
+	repo_read_index(repo);
 
-	if (update_modes(&reapply_opts.cone_mode, &reapply_opts.sparse_index))
+	if (update_modes(repo, &reapply_opts.cone_mode, &reapply_opts.sparse_index))
 		return 1;
 
-	return update_working_directory(NULL);
+	return update_working_directory(repo, NULL);
+}
+
+static char const * const builtin_sparse_checkout_clean_usage[] = {
+	"git sparse-checkout clean [-n|--dry-run]",
+	NULL
+};
+
+static int list_file_iterator(const char *path, const void *data)
+{
+	const char *msg = data;
+
+	printf(msg, path);
+	return 0;
+}
+
+static void list_every_file_in_dir(const char *msg,
+				   const char *directory)
+{
+	struct strbuf path = STRBUF_INIT;
+
+	strbuf_addstr(&path, directory);
+	fprintf(stderr, "list every file in %s\n", directory);
+
+	for_each_file_in_dir(&path, list_file_iterator, msg);
+	strbuf_release(&path);
+}
+
+static const char *msg_remove = N_("Removing %s\n");
+static const char *msg_would_remove = N_("Would remove %s\n");
+
+static int sparse_checkout_clean(int argc, const char **argv,
+				   const char *prefix,
+				   struct repository *repo)
+{
+	struct strbuf full_path = STRBUF_INIT;
+	const char *msg = msg_remove;
+	size_t worktree_len;
+	int force = 0, dry_run = 0, verbose = 0;
+	int require_force = 1;
+	struct unpack_trees_options o = { 0 };
+
+	struct option builtin_sparse_checkout_clean_options[] = {
+		OPT__DRY_RUN(&dry_run, N_("dry run")),
+		OPT__FORCE(&force, N_("force"), PARSE_OPT_NOCOMPLETE),
+		OPT__VERBOSE(&verbose, N_("report each affected file, not just directories")),
+		OPT_END(),
+	};
+
+	setup_work_tree();
+	if (!repo->settings.sparse_checkout)
+		die(_("must be in a sparse-checkout to clean directories"));
+	if (!repo->settings.sparse_checkout_cone)
+		die(_("must be in a cone-mode sparse-checkout to clean directories"));
+
+	argc = parse_options(argc, argv, prefix,
+			     builtin_sparse_checkout_clean_options,
+			     builtin_sparse_checkout_clean_usage, 0);
+
+	repo_config_get_bool(repo, "clean.requireforce", &require_force);
+	if (require_force && !force && !dry_run)
+		die(_("for safety, refusing to clean without one of --force or --dry-run"));
+
+	if (dry_run)
+		msg = msg_would_remove;
+
+	if (repo_read_index(repo) < 0)
+		die(_("failed to read index"));
+
+	o.verbose_update = verbose;
+	o.update = 0; /* skip modifying the worktree here. */
+	o.head_idx = -1;
+	o.src_index = o.dst_index = repo->index;
+	if (update_sparsity(&o, NULL))
+		warning(_("failed to reapply sparse-checkout patterns"));
+
+	if (convert_to_sparse(repo->index, SPARSE_INDEX_MEMORY_ONLY) ||
+	    repo->index->sparse_index == INDEX_EXPANDED)
+		die(_("failed to convert index to a sparse index; resolve merge conflicts and try again"));
+
+	strbuf_addstr(&full_path, repo->worktree);
+	strbuf_addch(&full_path, '/');
+	worktree_len = full_path.len;
+
+	for (size_t i = 0; i < repo->index->cache_nr; i++) {
+		struct cache_entry *ce = repo->index->cache[i];
+		if (!S_ISSPARSEDIR(ce->ce_mode))
+			continue;
+		strbuf_setlen(&full_path, worktree_len);
+		strbuf_add(&full_path, ce->name, ce->ce_namelen);
+
+		if (!is_directory(full_path.buf))
+			continue;
+
+		if (verbose)
+			list_every_file_in_dir(msg, ce->name);
+		else
+			printf(msg, ce->name);
+
+		if (dry_run <= 0 &&
+		    remove_dir_recursively(&full_path, 0))
+			warning_errno(_("failed to remove '%s'"), ce->name);
+	}
+
+	strbuf_release(&full_path);
+	return 0;
 }
 
 static char const * const builtin_sparse_checkout_disable_usage[] = {
@@ -927,7 +1037,7 @@ static char const * const builtin_sparse_checkout_disable_usage[] = {
 
 static int sparse_checkout_disable(int argc, const char **argv,
 				   const char *prefix,
-				   struct repository *repo UNUSED)
+				   struct repository *repo)
 {
 	static struct option builtin_sparse_checkout_disable_options[] = {
 		OPT_END(),
@@ -955,7 +1065,7 @@ static int sparse_checkout_disable(int argc, const char **argv,
 	 * are expecting to do that when disabling sparse-checkout.
 	 */
 	give_advice_on_expansion = 0;
-	repo_read_index(the_repository);
+	repo_read_index(repo);
 
 	memset(&pl, 0, sizeof(pl));
 	hashmap_init(&pl.recursive_hashmap, pl_hashmap_cmp, NULL, 0);
@@ -965,13 +1075,13 @@ static int sparse_checkout_disable(int argc, const char **argv,
 
 	add_pattern("/*", empty_base, 0, &pl, 0);
 
-	the_repository->settings.sparse_index = 0;
+	repo->settings.sparse_index = 0;
 
-	if (update_working_directory(&pl))
+	if (update_working_directory(repo, &pl))
 		die(_("error while refreshing working directory"));
 
 	clear_pattern_list(&pl);
-	return set_config(MODE_NO_PATTERNS);
+	return set_config(repo, MODE_NO_PATTERNS);
 }
 
 static char const * const builtin_sparse_checkout_check_rules_usage[] = {
@@ -986,14 +1096,17 @@ static struct sparse_checkout_check_rules_opts {
 	char *rules_file;
 } check_rules_opts;
 
-static int check_rules(struct pattern_list *pl, int null_terminated) {
+static int check_rules(struct repository *repo,
+		       struct pattern_list *pl,
+		       int null_terminated)
+{
 	struct strbuf line = STRBUF_INIT;
 	struct strbuf unquoted = STRBUF_INIT;
 	char *path;
 	int line_terminator = null_terminated ? 0 : '\n';
 	strbuf_getline_fn getline_fn = null_terminated ? strbuf_getline_nul
 		: strbuf_getline;
-	the_repository->index->sparse_checkout_patterns = pl;
+	repo->index->sparse_checkout_patterns = pl;
 	while (!getline_fn(&line, stdin)) {
 		path = line.buf;
 		if (!null_terminated && line.buf[0] == '"') {
@@ -1005,7 +1118,7 @@ static int check_rules(struct pattern_list *pl, int null_terminated) {
 			path = unquoted.buf;
 		}
 
-		if (path_in_sparse_checkout(path, the_repository->index))
+		if (path_in_sparse_checkout(path, repo->index))
 			write_name_quoted(path, stdout, line_terminator);
 	}
 	strbuf_release(&line);
@@ -1015,7 +1128,7 @@ static int check_rules(struct pattern_list *pl, int null_terminated) {
 }
 
 static int sparse_checkout_check_rules(int argc, const char **argv, const char *prefix,
-				       struct repository *repo UNUSED)
+				       struct repository *repo)
 {
 	static struct option builtin_sparse_checkout_check_rules_options[] = {
 		OPT_BOOL('z', NULL, &check_rules_opts.null_termination,
@@ -1054,7 +1167,7 @@ static int sparse_checkout_check_rules(int argc, const char **argv, const char *
 		free(sparse_filename);
 	}
 
-	ret = check_rules(&pl, check_rules_opts.null_termination);
+	ret = check_rules(repo, &pl, check_rules_opts.null_termination);
 	clear_pattern_list(&pl);
 	free(check_rules_opts.rules_file);
 	return ret;
@@ -1072,6 +1185,7 @@ int cmd_sparse_checkout(int argc,
 		OPT_SUBCOMMAND("set", &fn, sparse_checkout_set),
 		OPT_SUBCOMMAND("add", &fn, sparse_checkout_add),
 		OPT_SUBCOMMAND("reapply", &fn, sparse_checkout_reapply),
+		OPT_SUBCOMMAND("clean", &fn, sparse_checkout_clean),
 		OPT_SUBCOMMAND("disable", &fn, sparse_checkout_disable),
 		OPT_SUBCOMMAND("check-rules", &fn, sparse_checkout_check_rules),
 		OPT_END(),
@@ -1083,8 +1197,8 @@ int cmd_sparse_checkout(int argc,
 
 	git_config(git_default_config, NULL);
 
-	prepare_repo_settings(the_repository);
-	the_repository->settings.command_requires_full_index = 0;
+	prepare_repo_settings(repo);
+	repo->settings.command_requires_full_index = 0;
 
 	return fn(argc, argv, prefix, repo);
 }
diff --git a/dir.c b/dir.c
index d2b0a5aef6705e..2e567ff92746b1 100644
--- a/dir.c
+++ b/dir.c
@@ -30,6 +30,7 @@
 #include "read-cache-ll.h"
 #include "setup.h"
 #include "sparse-index.h"
+#include "strbuf.h"
 #include "submodule-config.h"
 #include "symlinks.h"
 #include "trace2.h"
@@ -87,6 +88,33 @@ struct dirent *readdir_skip_dot_and_dotdot(DIR *dirp)
 	return e;
 }
 
+int for_each_file_in_dir(struct strbuf *path, file_iterator fn, const void *data)
+{
+	struct dirent *e;
+	int res = 0;
+	size_t baselen = path->len;
+	DIR *dir = opendir(path->buf);
+
+	if (!dir)
+		return 0;
+
+	while (!res && (e = readdir_skip_dot_and_dotdot(dir)) != NULL) {
+		unsigned char dtype = get_dtype(e, path, 0);
+		strbuf_setlen(path, baselen);
+		strbuf_addstr(path, e->d_name);
+
+		if (dtype == DT_REG) {
+			res = fn(path->buf, data);
+		} else if (dtype == DT_DIR) {
+			strbuf_addch(path, '/');
+			res = for_each_file_in_dir(path, fn, data);
+		}
+	}
+
+	closedir(dir);
+	return res;
+}
+
 int count_slashes(const char *s)
 {
 	int cnt = 0;
diff --git a/dir.h b/dir.h
index d7e71aa8daa7d8..f4235cc12a2fe2 100644
--- a/dir.h
+++ b/dir.h
@@ -536,6 +536,20 @@ int get_sparse_checkout_patterns(struct pattern_list *pl);
  */
 int remove_dir_recursively(struct strbuf *path, int flag);
 
+/*
+ * This function pointer type is called on each file discovered in
+ * for_each_file_in_dir. The iteration stops if this method returns
+ * non-zero.
+ */
+typedef int (*file_iterator)(const char *path, const void *data);
+
+struct strbuf;
+/*
+ * Given a directory path, recursively visit each file within, including
+ * within subdirectories.
+ */
+int for_each_file_in_dir(struct strbuf *path, file_iterator fn, const void *data);
+
 /*
  * Tries to remove the path, along with leading empty directories so long as
  * those empty directories are not startup_info->original_cwd.  Ignores
diff --git a/sparse-index.c b/sparse-index.c
index ff33b8516b9f3d..cbf2bf618c37dc 100644
--- a/sparse-index.c
+++ b/sparse-index.c
@@ -31,7 +31,8 @@ int give_advice_on_expansion = 1;
 	"Your working directory likely has contents that are outside of\n"     \
 	"your sparse-checkout patterns. Use 'git sparse-checkout list' to\n"   \
 	"see your sparse-checkout definition and compare it to your working\n" \
-	"directory contents. Running 'git clean' may assist in this cleanup."
+	"directory contents. Running 'git sparse-checkout clean' may assist\n" \
+	"in this cleanup."
 
 struct modify_index_context {
 	struct index_state *write;
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index ab3a105ffff253..4b9078d90a616c 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -1050,5 +1050,135 @@ test_expect_success 'check-rules null termination' '
 	test_cmp expect actual
 '
 
+test_expect_success 'clean' '
+	git -C repo sparse-checkout set --cone deep/deeper1 &&
+	mkdir -p repo/deep/deeper2 repo/folder1/extra/inside &&
+	touch repo/deep/deeper2/file &&
+	touch repo/folder1/extra/inside/file &&
+
+	test_must_fail git -C repo sparse-checkout clean 2>err &&
+	grep "refusing to clean" err &&
+
+	git -C repo config clean.requireForce true &&
+	test_must_fail git -C repo sparse-checkout clean 2>err &&
+	grep "refusing to clean" err &&
+
+	cat >expect <<-\EOF &&
+	Would remove deep/deeper2/
+	Would remove folder1/
+	EOF
+
+	git -C repo sparse-checkout clean --dry-run >out &&
+	test_cmp expect out &&
+	test_path_exists repo/deep/deeper2 &&
+	test_path_exists repo/folder1/extra/inside/file &&
+
+	cat >expect <<-\EOF &&
+	Would remove deep/deeper2/file
+	Would remove folder1/extra/inside/file
+	EOF
+
+	git -C repo sparse-checkout clean --dry-run --verbose >out &&
+	test_cmp expect out &&
+
+	cat >expect <<-\EOF &&
+	Removing deep/deeper2/
+	Removing folder1/
+	EOF
+
+	git -C repo sparse-checkout clean -f >out &&
+	test_cmp expect out &&
+
+	test_path_is_missing repo/deep/deeper2 &&
+	test_path_is_missing repo/folder1
+'
+
+test_expect_success 'clean with staged sparse change' '
+	git -C repo sparse-checkout set --cone deep/deeper1 &&
+	mkdir repo/deep/deeper2 repo/folder1 repo/folder2 &&
+	touch repo/deep/deeper2/file &&
+	touch repo/folder1/file &&
+	echo dirty >repo/folder2/a &&
+
+	git -C repo add --sparse folder1/file &&
+
+	cat >expect <<-\EOF &&
+	Would remove deep/deeper2/
+	Would remove folder1/
+	EOF
+
+	git -C repo sparse-checkout clean --dry-run >out &&
+	test_cmp expect out &&
+	test_path_exists repo/deep/deeper2 &&
+	test_path_exists repo/folder1 &&
+	test_path_exists repo/folder2 &&
+
+	# deletes deep/deeper2/ but leaves folder1/ and folder2/
+	cat >expect <<-\EOF &&
+	Removing deep/deeper2/
+	Removing folder1/
+	EOF
+
+	# The previous test case checked the -f option, so
+	# test the config option in this one.
+	git -C repo config clean.requireForce false &&
+	git -C repo sparse-checkout clean >out &&
+	test_cmp expect out &&
+
+	test_path_is_missing repo/deep/deeper2 &&
+	test_path_is_missing repo/folder1 &&
+	test_path_exists repo/folder2
+'
+
+test_expect_success 'sparse-checkout operations with merge conflicts' '
+	git clone repo merge &&
+
+	(
+		cd merge &&
+		mkdir -p folder1/even/more/dirs &&
+		echo base >folder1/even/more/dirs/file &&
+		git add folder1 &&
+		git commit -m "base" &&
+
+		git checkout -b right&&
+		echo right >folder1/even/more/dirs/file &&
+		git commit -a -m "right" &&
+
+		git checkout -b left HEAD~1 &&
+		echo left >folder1/even/more/dirs/file &&
+		git commit -a -m "left" &&
+
+		git checkout -b merge &&
+
+		touch deep/deeper2/extra &&
+		git sparse-checkout set deep/deeper1 2>err &&
+		grep "contains untracked files" err &&
+		test_path_exists deep/deeper2/extra &&
+
+		test_must_fail git merge -m "will-conflict" right &&
+
+		test_must_fail git sparse-checkout clean -f 2>err &&
+		grep "failed to convert index to a sparse index" err &&
+
+		echo merged >folder1/even/more/dirs/file &&
+		git add --sparse folder1 &&
+		git merge --continue &&
+
+		test_path_exists folder1/even/more/dirs/file &&
+		test_path_exists deep/deeper2/extra &&
+
+		cat >expect <<-\EOF &&
+		Removing deep/deeper2/
+		Removing folder1/
+		EOF
+
+		# clean does not remove the file, because the
+		# SKIP_WORKTREE bit was not cleared by the merge command.
+		git sparse-checkout clean -f >out &&
+		test_cmp expect out &&
+		test_path_is_missing folder1 &&
+		test_path_is_missing deep/deeper2
+	)
+'
 
 test_done
diff --git a/unpack-trees.c b/unpack-trees.c
index 0e9813bddf048e..b8814af1b07c0d 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -2138,7 +2138,7 @@ enum update_sparsity_result update_sparsity(struct unpack_trees_options *o,
 	index_state_init(&o->internal.result, o->src_index->repo);
 
 	/* Sanity checks */
-	if (!o->update || o->index_only || o->skip_sparse_checkout)
+	if (o->index_only || o->skip_sparse_checkout)
 		BUG("update_sparsity() is for reflecting sparsity patterns in working directory");
 	if (o->src_index != o->dst_index || o->fn)
 		BUG("update_sparsity() called wrong");