diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 9c338d33ea263b..5518ed47f6c256 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -1,4 +1,5 @@
 #include "builtin.h"
+#include "cache.h"
 #include "config.h"
 #include "dir.h"
 #include "parse-options.h"
@@ -401,6 +402,7 @@ static int update_modes(int *cone_mode, int *sparse_index)
 		core_sparse_checkout_cone = 1;
 	} else {
 		mode = MODE_ALL_PATTERNS;
+		core_sparse_checkout_cone = 0;
 	}
 	if (record_mode && set_config(mode))
 		return 1;
@@ -681,18 +683,76 @@ static int modify_pattern_list(int argc, const char **argv, int use_stdin,
 	return result;
 }
 
+static void sanitize_paths(int argc, const char **argv,
+			   const char *prefix, int skip_checks)
+{
+	int i;
+
+	if (!argc)
+		return;
+
+	if (prefix && *prefix && core_sparse_checkout_cone) {
+		/*
+		 * The args are not pathspecs, so unfortunately we
+		 * cannot imitate how cmd_add() uses parse_pathspec().
+		 */
+		int prefix_len = strlen(prefix);
+
+		for (i = 0; i < argc; i++)
+			argv[i] = prefix_path(prefix, prefix_len, argv[i]);
+	}
+
+	if (skip_checks)
+		return;
+
+	if (prefix && *prefix && !core_sparse_checkout_cone)
+		die(_("please run from the toplevel directory in non-cone mode"));
+
+	if (core_sparse_checkout_cone) {
+		for (i = 0; i < argc; i++) {
+			if (argv[i][0] == '/')
+				die(_("specify directories rather than patterns (no leading slash)"));
+			if (argv[i][0] == '!')
+				die(_("specify directories rather than patterns.  If your directory starts with a '!', pass --skip-checks"));
+			if (strpbrk(argv[i], "*?[]"))
+				die(_("specify directories rather than patterns.  If your directory really has any of '*?[]\\' in it, pass --skip-checks"));
+		}
+	}
+
+	for (i = 0; i < argc; i++) {
+		struct cache_entry *ce;
+		struct index_state *index = the_repository->index;
+		int pos = index_name_pos(index, argv[i], strlen(argv[i]));
+
+		if (pos < 0)
+			continue;
+		ce = index->cache[pos];
+		if (S_ISSPARSEDIR(ce->ce_mode))
+			continue;
+
+		if (core_sparse_checkout_cone)
+			die(_("'%s' is not a directory; to treat it as a directory anyway, rerun with --skip-checks"), argv[i]);
+		else
+			warning(_("pass a leading slash before paths such as '%s' if you want a single file (see NON-CONE PROBLEMS in the git-sparse-checkout manual)."), argv[i]);
+	}
+}
+
 static char const * const builtin_sparse_checkout_add_usage[] = {
-	N_("git sparse-checkout add (--stdin | <patterns>)"),
+	N_("git sparse-checkout add [--skip-checks] (--stdin | <patterns>)"),
 	NULL
 };
 
 static struct sparse_checkout_add_opts {
+	int skip_checks;
 	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_F(0, "skip-checks", &add_opts.skip_checks,
+			   N_("skip some sanity checks on the given paths that might give false positives"),
+			   PARSE_OPT_NONEG),
 		OPT_BOOL(0, "stdin", &add_opts.use_stdin,
 			 N_("read patterns from standard in")),
 		OPT_END(),
@@ -708,17 +768,20 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 			     builtin_sparse_checkout_add_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
+	sanitize_paths(argc, argv, prefix, add_opts.skip_checks);
+
 	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 [--[no-]cone] [--[no-]sparse-index] (--stdin | <patterns>)"),
+	N_("git sparse-checkout set [--[no-]cone] [--[no-]sparse-index] [--skip-checks] (--stdin | <patterns>)"),
 	NULL
 };
 
 static struct sparse_checkout_set_opts {
 	int cone_mode;
 	int sparse_index;
+	int skip_checks;
 	int use_stdin;
 } set_opts;
 
@@ -732,6 +795,9 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 			 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, "skip-checks", &set_opts.skip_checks,
+			   N_("skip some sanity checks on the given paths that might give false positives"),
+			   PARSE_OPT_NONEG),
 		OPT_BOOL_F(0, "stdin", &set_opts.use_stdin,
 			   N_("read patterns from standard in"),
 			   PARSE_OPT_NONEG),
@@ -759,6 +825,8 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 	if (!core_sparse_checkout_cone && argc == 0) {
 		argv = default_patterns;
 		argc = default_patterns_nr;
+	} else {
+		sanitize_paths(argc, argv, prefix, set_opts.skip_checks);
 	}
 
 	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
@@ -787,15 +855,15 @@ static int sparse_checkout_reapply(int argc, const char **argv)
 	if (!core_apply_sparse_checkout)
 		die(_("must be in a sparse-checkout to reapply sparsity patterns"));
 
+	reapply_opts.cone_mode = -1;
+	reapply_opts.sparse_index = -1;
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_reapply_options,
 			     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;
 
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 502d42d183a098..9a900310186d38 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -510,6 +510,37 @@ test_expect_failure 'sparse-checkout reapply' '
 	git -C tweak sparse-checkout disable
 '
 
+test_expect_success 'reapply can handle config options' '
+	git -C repo sparse-checkout init --cone --no-sparse-index &&
+	git -C repo config --worktree --list >actual &&
+	cat >expect <<-\EOF &&
+	core.sparsecheckout=true
+	core.sparsecheckoutcone=true
+	index.sparse=false
+	EOF
+	test_cmp expect actual &&
+
+	git -C repo sparse-checkout reapply --no-cone --no-sparse-index &&
+	git -C repo config --worktree --list >actual &&
+	cat >expect <<-\EOF &&
+	core.sparsecheckout=true
+	core.sparsecheckoutcone=false
+	index.sparse=false
+	EOF
+	test_cmp expect actual &&
+
+	git -C repo sparse-checkout reapply --cone --sparse-index &&
+	git -C repo config --worktree --list >actual &&
+	cat >expect <<-\EOF &&
+	core.sparsecheckout=true
+	core.sparsecheckoutcone=true
+	index.sparse=true
+	EOF
+	test_cmp expect actual &&
+
+	git -C repo sparse-checkout disable
+'
+
 test_expect_success 'cone mode: set with core.ignoreCase=true' '
 	rm repo/.git/info/sparse-checkout &&
 	git -C repo sparse-checkout init --cone &&
@@ -549,7 +580,7 @@ test_expect_success 'different sparse-checkouts with worktrees' '
 '
 
 test_expect_success 'set using filename keeps file on-disk' '
-	git -C repo sparse-checkout set a deep &&
+	git -C repo sparse-checkout set --skip-checks a deep &&
 	cat >expect <<-\EOF &&
 	/*
 	!/*/
@@ -660,7 +691,7 @@ test_expect_success BSLASHPSPEC 'pattern-checks: escaped characters' '
 	git -C escaped reset --hard $COMMIT &&
 	check_files escaped "a deep folder1 folder2 zbad\\dir zdoes*exist" zglob[!a]? &&
 	git -C escaped sparse-checkout init --cone &&
-	git -C escaped sparse-checkout set zbad\\dir/bogus "zdoes*not*exist" "zdoes*exist" "zglob[!a]?" &&
+	git -C escaped sparse-checkout set --skip-checks zbad\\dir/bogus "zdoes*not*exist" "zdoes*exist" "zglob[!a]?" &&
 	cat >expect <<-\EOF &&
 	/*
 	!/*/
@@ -785,4 +816,59 @@ test_expect_success 'malformed cone-mode patterns' '
 	grep "warning: disabling cone pattern matching" err
 '
 
+test_expect_success 'set from subdir pays attention to prefix' '
+	git -C repo sparse-checkout disable &&
+	git -C repo/deep sparse-checkout set --cone deeper2 ../folder1 &&
+
+	git -C repo sparse-checkout list >actual &&
+
+	cat >expect <<-\EOF &&
+	deep/deeper2
+	folder1
+	EOF
+	test_cmp expect actual
+'
+
+test_expect_success 'add from subdir pays attention to prefix' '
+	git -C repo sparse-checkout set --cone deep/deeper2 &&
+	git -C repo/deep sparse-checkout add deeper1/deepest ../folder1 &&
+
+	git -C repo sparse-checkout list >actual &&
+
+	cat >expect <<-\EOF &&
+	deep/deeper1/deepest
+	deep/deeper2
+	folder1
+	EOF
+	test_cmp expect actual
+'
+
+test_expect_success 'set from subdir in non-cone mode throws an error' '
+	git -C repo sparse-checkout disable &&
+	test_must_fail git -C repo/deep sparse-checkout set --no-cone deeper2 ../folder1 2>error &&
+
+	grep "run from the toplevel directory in non-cone mode" error
+'
+
+test_expect_success 'set from subdir in non-cone mode throws an error' '
+	git -C repo sparse-checkout set --no-cone deep/deeper2 &&
+	test_must_fail git -C repo/deep sparse-checkout add deeper1/deepest ../folder1 2>error &&
+
+	grep "run from the toplevel directory in non-cone mode" error
+'
+
+test_expect_success 'by default, cone mode will error out when passed files' '
+	git -C repo sparse-checkout reapply --cone &&
+	test_must_fail git -C repo sparse-checkout add .gitignore 2>error &&
+
+	grep ".gitignore.*is not a directory" error
+'
+
+test_expect_success 'by default, non-cone mode will warn on individual files' '
+	git -C repo sparse-checkout reapply --no-cone &&
+	git -C repo sparse-checkout add .gitignore 2>warning &&
+
+	grep "pass a leading slash before paths.*if you want a single file" warning
+'
+
 test_done