diff --git a/Documentation/config.txt b/Documentation/config.txt
index bf3e512921f..f0fb25a371c 100644
--- a/Documentation/config.txt
+++ b/Documentation/config.txt
@@ -503,6 +503,8 @@ include::config/sequencer.txt[]
 
 include::config/showbranch.txt[]
 
+include::config/sparse.txt[]
+
 include::config/splitindex.txt[]
 
 include::config/ssh.txt[]
diff --git a/Documentation/config/sparse.txt b/Documentation/config/sparse.txt
new file mode 100644
index 00000000000..aff49a8d3a3
--- /dev/null
+++ b/Documentation/config/sparse.txt
@@ -0,0 +1,27 @@
+sparse.expectFilesOutsideOfPatterns::
+	Typically with sparse checkouts, files not matching any
+	sparsity patterns are marked with a SKIP_WORKTREE bit in the
+	index and are missing from the working tree.  Accordingly, Git
+	will ordinarily check whether files with the SKIP_WORKTREE bit
+	are in fact present in the working tree contrary to
+	expectations.  If Git finds any, it marks those paths as
+	present by clearing the relevant SKIP_WORKTREE bits.  This
+	option can be used to tell Git that such
+	present-despite-skipped files are expected and to stop
+	checking for them.
++
+The default is `false`, which allows Git to automatically recover
+from the list of files in the index and working tree falling out of
+sync.
++
+Set this to `true` if you are in a setup where some external factor
+relieves Git of the responsibility for maintaining the consistency
+between the presence of working tree files and sparsity patterns.  For
+example, if you have a Git-aware virtual file system that has a robust
+mechanism for keeping the working tree and the sparsity patterns up to
+date based on access patterns.
++
+Regardless of this setting, Git does not check for
+present-despite-skipped files unless sparse checkout is enabled, so
+this config option has no effect unless `core.sparseCheckout` is
+`true`.
diff --git a/Documentation/git-read-tree.txt b/Documentation/git-read-tree.txt
index 8c3aceb8324..99bb387134d 100644
--- a/Documentation/git-read-tree.txt
+++ b/Documentation/git-read-tree.txt
@@ -375,9 +375,14 @@ have finished your work-in-progress), attempt the merge again.
 SPARSE CHECKOUT
 ---------------
 
+Note: The `update-index` and `read-tree` primitives for supporting the
+skip-worktree bit predated the introduction of
+linkgit:git-sparse-checkout[1].  Users are encouraged to use
+`sparse-checkout` in preference to these low-level primitives.
+
 "Sparse checkout" allows populating the working directory sparsely.
-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.
+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.
 
 'git read-tree' and other merge-based commands ('git merge', 'git
 checkout'...) can help maintaining the skip-worktree bitmap and working
@@ -385,7 +390,8 @@ directory update. `$GIT_DIR/info/sparse-checkout` is used to
 define the skip-worktree reference bitmap. When 'git read-tree' needs
 to update the working directory, it resets the skip-worktree bit in the index
 based on this file, which uses the same syntax as .gitignore files.
-If an entry matches a pattern in this file, skip-worktree will not be
+If an entry matches a pattern in this file, or the entry corresponds to
+a file present in the working tree, then skip-worktree will not be
 set on that entry. Otherwise, skip-worktree will be set.
 
 Then it compares the new skip-worktree value with the previous one. If
diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index 94dad137b96..88e55f432f3 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -3,9 +3,7 @@ git-sparse-checkout(1)
 
 NAME
 ----
-git-sparse-checkout - Initialize and modify the sparse-checkout
-configuration, which reduces the checkout to a set of paths
-given by a list of patterns.
+git-sparse-checkout - Reduce your working tree to a subset of tracked files
 
 
 SYNOPSIS
@@ -17,8 +15,20 @@ SYNOPSIS
 DESCRIPTION
 -----------
 
-Initialize and modify the sparse-checkout configuration, which reduces
-the checkout to a set of paths given by a list of patterns.
+This command is used to create sparse checkouts, which means that it
+changes the working tree from having all tracked files present, to only
+have a subset of them.  It can also switch which subset of files are
+present, or undo and go back to having all tracked files present in the
+working copy.
+
+The subset of files is chosen by providing a list of directories in
+cone mode (which is recommended), or by providing a list of patterns
+in non-cone mode.
+
+When in a sparse-checkout, other Git commands behave a bit differently.
+For example, switching branches will not update paths outside the
+sparse-checkout directories/patterns, and `git commit -a` will not record
+paths outside the sparse-checkout directories/patterns as deleted.
 
 THIS COMMAND IS EXPERIMENTAL. ITS BEHAVIOR, AND THE BEHAVIOR OF OTHER
 COMMANDS IN THE PRESENCE OF SPARSE-CHECKOUTS, WILL LIKELY CHANGE IN
@@ -28,7 +38,7 @@ THE FUTURE.
 COMMANDS
 --------
 'list'::
-	Describe the patterns in the sparse-checkout file.
+	Describe the directories or patterns in the sparse-checkout file.
 
 'set'::
 	Enable the necessary sparse-checkout config settings
@@ -46,20 +56,26 @@ the 'set' subcommand are stored in the worktree-specific sparse-checkout
 file. See linkgit:git-worktree[1] and the documentation of
 `extensions.worktreeConfig` in linkgit:git-config[1] for more details.
 +
-When the `--stdin` option is provided, the patterns are read from
-standard in as a newline-delimited list instead of from the arguments.
+When the `--stdin` option is provided, the directories or patterns are
+read from standard in as a newline-delimited list instead of from the
+arguments.
 +
 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.
+input list is considered a list of directories.  This allows for
+better performance with a limited set of patterns (see 'CONE PATTERN
+SET' below).  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.  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. This may become the default in the
+future; --no-cone can be passed to request non-cone mode.
++
+When `--no-cone` is passed or `core.sparseCheckoutCone` is not enabled,
+the input list is considered a list of patterns.  This mode is harder
+to use and less performant, and is thus not recommended.  See the
+"Sparse Checkout" section of linkgit:git-read-tree[1] and the "Pattern
+Set" sections below for more details.
 +
 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
@@ -77,11 +93,10 @@ understand the sparse directory entries index extension and may fail to
 interact with your repository until it is disabled.
 
 'add'::
-	Update the sparse-checkout file to include additional patterns.
-	By default, these patterns are read from the command-line arguments,
-	but they can be read from stdin using the `--stdin` option. When
-	`core.sparseCheckoutCone` is enabled, the given patterns are interpreted
-	as directory names as in the 'set' subcommand.
+	Update the sparse-checkout file to include additional directories
+	(in cone mode) or patterns (in non-cone mode).  By default, these
+	directories or patterns are read from the command-line arguments,
+	but they can be read from stdin using the `--stdin` option.
 
 'reapply'::
 	Reapply the sparsity pattern rules to paths in the working tree.
@@ -125,13 +140,14 @@ decreased in utility.
 SPARSE CHECKOUT
 ---------------
 
-"Sparse checkout" allows populating the working directory sparsely.
-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 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.
+"Sparse checkout" allows populating the working directory sparsely.  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, and the file is not present in the working tree,
+then its absence is ignored. 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.
 
 The `$GIT_DIR/info/sparse-checkout` file is used to define the
 skip-worktree reference bitmap. When Git updates the working
diff --git a/Documentation/git-update-index.txt b/Documentation/git-update-index.txt
index 2853f168d97..568dbfe76b8 100644
--- a/Documentation/git-update-index.txt
+++ b/Documentation/git-update-index.txt
@@ -351,6 +351,10 @@ unchanged".  Note that "assume unchanged" bit is *not* set if
 the index (use `git update-index --really-refresh` if you want
 to mark them as "assume unchanged").
 
+Sometimes users confuse the assume-unchanged bit with the
+skip-worktree bit.  See the final paragraph in the "Skip-worktree bit"
+section below for an explanation of the differences.
+
 
 EXAMPLES
 --------
@@ -392,22 +396,47 @@ M foo.c
 SKIP-WORKTREE BIT
 -----------------
 
-Skip-worktree bit can be defined in one (long) sentence: When reading
-an entry, if it is marked as skip-worktree, then Git pretends its
-working directory version is up to date and read the index version
-instead.
+Skip-worktree bit can be defined in one (long) sentence: Tell git to
+avoid writing the file to the working directory when reasonably
+possible, and treat the file as unchanged when it is not
+present in the working directory.
 
-To elaborate, "reading" means checking for file existence, reading
-file attributes or file content. The working directory version may be
-present or absent. If present, its content may match against the index
-version or not. Writing is not affected by this bit, content safety
-is still first priority. Note that Git _can_ update working directory
-file, that is marked skip-worktree, if it is safe to do so (i.e.
-working directory version matches index version)
+Note that not all git commands will pay attention to this bit, and
+some only partially support it.
+
+The update-index flags and the read-tree capabilities relating to the
+skip-worktree bit predated the introduction of the
+linkgit:git-sparse-checkout[1] command, which provides a much easier
+way to configure and handle the skip-worktree bits.  If you want to
+reduce your working tree to only deal with a subset of the files in
+the repository, we strongly encourage the use of
+linkgit:git-sparse-checkout[1] in preference to the low-level
+update-index and read-tree primitives.
+
+The primary purpose of the skip-worktree bit is to enable sparse
+checkouts, i.e. to have working directories with only a subset of
+paths present.  When the skip-worktree bit is set, Git commands (such
+as `switch`, `pull`, `merge`) will avoid writing these files.
+However, these commands will sometimes write these files anyway in
+important cases such as conflicts during a merge or rebase.  Git
+commands will also avoid treating the lack of such files as an
+intentional deletion; for example `git add -u` will not not stage a
+deletion for these files and `git commit -a` will not make a commit
+deleting them either.
 
 Although this bit looks similar to assume-unchanged bit, its goal is
-different from assume-unchanged bit's. Skip-worktree also takes
-precedence over assume-unchanged bit when both are set.
+different.  The assume-unchanged bit is for leaving the file in the
+working tree but having Git omit checking it for changes and presuming
+that the file has not been changed (though if it can determine without
+stat'ing the file that it has changed, it is free to record the
+changes).  skip-worktree tells Git to ignore the absence of the file,
+avoid updating it when possible with commands that normally update
+much of the working directory (e.g. `checkout`, `switch`, `pull`,
+etc.), and not have its absence be recorded in commits.  Note that in
+sparse checkouts (setup by `git sparse-checkout` or by configuring
+core.sparseCheckout to true), if a file is marked as skip-worktree in
+the index but is found in the working tree, Git will clear the
+skip-worktree bit for that file.
 
 SPLIT INDEX
 -----------
diff --git a/cache.h b/cache.h
index 04d4d2db25c..9e3d423b951 100644
--- a/cache.h
+++ b/cache.h
@@ -1003,6 +1003,7 @@ extern const char *core_fsmonitor;
 
 extern int core_apply_sparse_checkout;
 extern int core_sparse_checkout_cone;
+extern int sparse_expect_files_outside_of_patterns;
 
 /*
  * Returns the boolean value of $GIT_OPTIONAL_LOCKS (or the default value).
diff --git a/config.c b/config.c
index 383b1a4885b..e78397725c9 100644
--- a/config.c
+++ b/config.c
@@ -1654,6 +1654,17 @@ static int git_default_core_config(const char *var, const char *value, void *cb)
 	return platform_core_config(var, value, cb);
 }
 
+static int git_default_sparse_config(const char *var, const char *value)
+{
+	if (!strcmp(var, "sparse.expectfilesoutsideofpatterns")) {
+		sparse_expect_files_outside_of_patterns = git_config_bool(var, value);
+		return 0;
+	}
+
+	/* Add other config variables here and to Documentation/config/sparse.txt. */
+	return 0;
+}
+
 static int git_default_i18n_config(const char *var, const char *value)
 {
 	if (!strcmp(var, "i18n.commitencoding"))
@@ -1785,6 +1796,9 @@ int git_default_config(const char *var, const char *value, void *cb)
 		return 0;
 	}
 
+	if (starts_with(var, "sparse."))
+		return git_default_sparse_config(var, value);
+
 	/* Add other config variables here and to Documentation/config.txt. */
 	return 0;
 }
diff --git a/environment.c b/environment.c
index fd0501e77a5..fb55bf61290 100644
--- a/environment.c
+++ b/environment.c
@@ -70,6 +70,7 @@ char *notes_ref_name;
 int grafts_replace_parents = 1;
 int core_apply_sparse_checkout;
 int core_sparse_checkout_cone;
+int sparse_expect_files_outside_of_patterns;
 int merge_log_config = -1;
 int precomposed_unicode = -1; /* see probe_utf8_pathname_composition() */
 unsigned long pack_size_limit_cfg;
diff --git a/repository.c b/repository.c
index 34610c5a33e..dddee32258f 100644
--- a/repository.c
+++ b/repository.c
@@ -301,6 +301,13 @@ int repo_read_index(struct repository *repo)
 	if (repo->settings.command_requires_full_index)
 		ensure_full_index(repo->index);
 
+	/*
+	 * If sparse checkouts are in use, check whether paths with the
+	 * SKIP_WORKTREE attribute are missing from the worktree; if not,
+	 * clear that attribute for that path.
+	 */
+	clear_skip_worktree_from_present_files(repo->index);
+
 	return res;
 }
 
diff --git a/sparse-index.c b/sparse-index.c
index fdbe97b9769..8636af72de5 100644
--- a/sparse-index.c
+++ b/sparse-index.c
@@ -337,6 +337,80 @@ void ensure_correct_sparsity(struct index_state *istate)
 		ensure_full_index(istate);
 }
 
+static int path_found(const char *path, const char **dirname, size_t *dir_len,
+		      int *dir_found)
+{
+	struct stat st;
+	char *newdir;
+	char *tmp;
+
+	/*
+	 * If dirname corresponds to a directory that doesn't exist, and this
+	 * path starts with dirname, then path can't exist.
+	 */
+	if (!*dir_found && !memcmp(path, *dirname, *dir_len))
+		return 0;
+
+	/*
+	 * If path itself exists, return 1.
+	 */
+	if (!lstat(path, &st))
+		return 1;
+
+	/*
+	 * Otherwise, path does not exist so we'll return 0...but we'll first
+	 * determine some info about its parent directory so we can avoid
+	 * lstat calls for future cache entries.
+	 */
+	newdir = strrchr(path, '/');
+	if (!newdir)
+		return 0; /* Didn't find a parent dir; just return 0 now. */
+
+	/*
+	 * If path starts with directory (which we already lstat'ed and found),
+	 * then no need to lstat parent directory again.
+	 */
+	if (*dir_found && *dirname && memcmp(path, *dirname, *dir_len))
+		return 0;
+
+	/* Free previous dirname, and cache path's dirname */
+	*dirname = path;
+	*dir_len = newdir - path + 1;
+
+	tmp = xstrndup(path, *dir_len);
+	*dir_found = !lstat(tmp, &st);
+	free(tmp);
+
+	return 0;
+}
+
+void clear_skip_worktree_from_present_files(struct index_state *istate)
+{
+	const char *last_dirname = NULL;
+	size_t dir_len = 0;
+	int dir_found = 1;
+
+	int i;
+
+	if (!core_apply_sparse_checkout ||
+	    sparse_expect_files_outside_of_patterns)
+		return;
+
+restart:
+	for (i = 0; i < istate->cache_nr; i++) {
+		struct cache_entry *ce = istate->cache[i];
+
+		if (ce_skip_worktree(ce) &&
+		    path_found(ce->name, &last_dirname, &dir_len, &dir_found)) {
+			if (S_ISSPARSEDIR(ce->ce_mode)) {
+				ensure_full_index(istate);
+				goto restart;
+			}
+			ce->ce_flags &= ~CE_SKIP_WORKTREE;
+		}
+	}
+}
+
 /*
  * This static global helps avoid infinite recursion between
  * expand_to_path() and index_file_exists().
diff --git a/sparse-index.h b/sparse-index.h
index 656bd835b25..633d4fb7e31 100644
--- a/sparse-index.h
+++ b/sparse-index.h
@@ -5,6 +5,7 @@ struct index_state;
 #define SPARSE_INDEX_MEMORY_ONLY (1 << 0)
 int convert_to_sparse(struct index_state *istate, int flags);
 void ensure_correct_sparsity(struct index_state *istate);
+void clear_skip_worktree_from_present_files(struct index_state *istate);
 
 /*
  * Some places in the codebase expect to search for a specific path.
diff --git a/t/t1011-read-tree-sparse-checkout.sh b/t/t1011-read-tree-sparse-checkout.sh
index 24092c09a95..dd957be1b78 100755
--- a/t/t1011-read-tree-sparse-checkout.sh
+++ b/t/t1011-read-tree-sparse-checkout.sh
@@ -187,11 +187,32 @@ test_expect_success 'read-tree updates worktree, absent case' '
 	test ! -f init.t
 '
 
+test_expect_success 'read-tree will not throw away dirty changes, non-sparse' '
+	echo "/*" >.git/info/sparse-checkout &&
+	read_tree_u_must_succeed -m -u HEAD &&
+
+	echo dirty >init.t &&
+	read_tree_u_must_fail -m -u HEAD^ &&
+	test_path_is_file init.t &&
+	grep -q dirty init.t
+'
+
+test_expect_success 'read-tree will not throw away dirty changes, sparse' '
+	echo "/*" >.git/info/sparse-checkout &&
+	read_tree_u_must_succeed -m -u HEAD &&
+
+	echo dirty >init.t &&
+	echo sub/added >.git/info/sparse-checkout &&
+	read_tree_u_must_fail -m -u HEAD^ &&
+	test_path_is_file init.t &&
+	grep -q dirty init.t
+'
+
 test_expect_success 'read-tree updates worktree, dirty case' '
 	echo sub/added >.git/info/sparse-checkout &&
 	git checkout -f top &&
 	echo dirty >init.t &&
-	read_tree_u_must_succeed -m -u HEAD^ &&
+	read_tree_u_must_fail -m -u HEAD^ &&
 	grep -q dirty init.t &&
 	rm init.t
 '
diff --git a/t/t1090-sparse-checkout-scope.sh b/t/t1090-sparse-checkout-scope.sh
index 3deb4901874..d1833c0f31b 100755
--- a/t/t1090-sparse-checkout-scope.sh
+++ b/t/t1090-sparse-checkout-scope.sh
@@ -52,6 +52,25 @@ test_expect_success 'return to full checkout of main' '
 	test "$(cat b)" = "modified"
 '
 
+test_expect_success 'skip-worktree on files outside sparse patterns' '
+	git sparse-checkout disable &&
+	git sparse-checkout set --no-cone "a*" &&
+	git checkout-index --all --ignore-skip-worktree-bits &&
+
+	git ls-files -t >output &&
+	! grep ^S output >actual &&
+	test_must_be_empty actual &&
+
+	test_config sparse.expectFilesOutsideOfPatterns true &&
+	cat <<-\EOF >expect &&
+	S b
+	S c
+	EOF
+	git ls-files -t >output &&
+	grep ^S output >actual &&
+	test_cmp expect actual
+'
+
 test_expect_success 'in partial clone, sparse checkout only fetches needed blobs' '
 	test_create_repo server &&
 	git clone "file://$(pwd)/server" client &&
diff --git a/t/t1092-sparse-checkout-compatibility.sh b/t/t1092-sparse-checkout-compatibility.sh
index f3a059e5af5..2a04b532f91 100755
--- a/t/t1092-sparse-checkout-compatibility.sh
+++ b/t/t1092-sparse-checkout-compatibility.sh
@@ -367,7 +367,7 @@ test_expect_success 'status/add: outside sparse cone' '
 	write_script edit-contents <<-\EOF &&
 	echo text >>$1
 	EOF
-	run_on_sparse ../edit-contents folder1/a &&
+	run_on_all ../edit-contents folder1/a &&
 	run_on_all ../edit-contents folder1/new &&
 
 	test_sparse_match git status --porcelain=v2 &&
@@ -376,8 +376,8 @@ test_expect_success 'status/add: outside sparse cone' '
 	test_sparse_match test_must_fail git add folder1/a &&
 	grep "Disable or modify the sparsity rules" sparse-checkout-err &&
 	test_sparse_unstaged folder1/a &&
-	test_sparse_match test_must_fail git add --refresh folder1/a &&
-	grep "Disable or modify the sparsity rules" sparse-checkout-err &&
+	test_all_match git add --refresh folder1/a &&
+	test_must_be_empty sparse-checkout-err &&
 	test_sparse_unstaged folder1/a &&
 	test_sparse_match test_must_fail git add folder1/new &&
 	grep "Disable or modify the sparsity rules" sparse-checkout-err &&
@@ -643,11 +643,11 @@ test_expect_success 'update-index modify outside sparse definition' '
 	run_on_sparse cp ../initial-repo/folder1/a folder1/a &&
 	run_on_all ../edit-contents folder1/a &&
 
-	# If file has skip-worktree enabled, update-index does not modify the
-	# index entry
-	test_sparse_match git update-index folder1/a &&
-	test_sparse_match git status --porcelain=v2 &&
-	test_must_be_empty sparse-checkout-out &&
+	# If file has skip-worktree enabled, but the file is present, it is
+	# treated the same as if skip-worktree is disabled
+	test_all_match git status --porcelain=v2 &&
+	test_all_match git update-index folder1/a &&
+	test_all_match git status --porcelain=v2 &&
 
 	# When skip-worktree is disabled (even on files outside sparse cone), file
 	# is updated in the index
@@ -1331,30 +1331,27 @@ test_expect_success 'ls-files' '
 	test_cmp dense sparse &&
 
 	# Set up a strange condition of having a file edit
-	# outside of the sparse-checkout cone. This is just
-	# to verify that sparse-checkout and sparse-index
-	# behave the same in this case.
+	# outside of the sparse-checkout cone. We want to verify
+	# that all modes handle this the same, and detect the
+	# modification.
 	write_script edit-content <<-\EOF &&
-	mkdir folder1 &&
+	mkdir -p folder1 &&
 	echo content >>folder1/a
 	EOF
-	run_on_sparse ../edit-content &&
+	run_on_all ../edit-content &&
 
-	# ls-files does not currently notice modified files whose
-	# cache entries are marked SKIP_WORKTREE. This may change
-	# in the future, but here we test that sparse index does
-	# not accidentally create a change of behavior.
-	test_sparse_match git ls-files --modified &&
-	test_must_be_empty sparse-checkout-out &&
-	test_must_be_empty sparse-index-out &&
+	test_all_match git ls-files --modified &&
 
 	git -C sparse-index ls-files --sparse --modified >sparse-index-out &&
-	test_must_be_empty sparse-index-out &&
+	cat >expect <<-\EOF &&
+	folder1/a
+	EOF
+	test_cmp expect sparse-index-out &&
 
 	# Add folder1 to the sparse-checkout cone and
 	# check that ls-files shows the expanded files.
 	test_sparse_match git sparse-checkout add folder1 &&
-	test_sparse_match git ls-files --modified &&
+	test_all_match git ls-files --modified &&
 
 	test_all_match git ls-files &&
 	git -C sparse-index ls-files --sparse >actual &&
diff --git a/t/t3705-add-sparse-checkout.sh b/t/t3705-add-sparse-checkout.sh
index 81f3384eeed..95609046c61 100755
--- a/t/t3705-add-sparse-checkout.sh
+++ b/t/t3705-add-sparse-checkout.sh
@@ -19,6 +19,7 @@ setup_sparse_entry () {
 	fi &&
 	git add sparse_entry &&
 	git update-index --skip-worktree sparse_entry &&
+	git config core.sparseCheckout false &&
 	git commit --allow-empty -m "ensure sparse_entry exists at HEAD" &&
 	SPARSE_ENTRY_BLOB=$(git rev-parse :sparse_entry)
 }
@@ -126,6 +127,7 @@ test_expect_success 'git add --chmod does not update sparse entries' '
 '
 
 test_expect_success 'git add --renormalize does not update sparse entries' '
+	test_when_finished rm .gitattributes &&
 	test_config core.autocrlf false &&
 	setup_sparse_entry "LINEONE\r\nLINETWO\r\n" &&
 	echo "sparse_entry text=auto" >.gitattributes &&
diff --git a/t/t6428-merge-conflicts-sparse.sh b/t/t6428-merge-conflicts-sparse.sh
index 7e8bf497f82..142c9aaabc5 100755
--- a/t/t6428-merge-conflicts-sparse.sh
+++ b/t/t6428-merge-conflicts-sparse.sh
@@ -112,7 +112,7 @@ test_expect_success 'conflicting entries written to worktree even if sparse' '
 	)
 '
 
-test_expect_merge_algorithm failure success 'present-despite-SKIP_WORKTREE handled reasonably' '
+test_expect_success 'present-despite-SKIP_WORKTREE handled reasonably' '
 	test_setup_numerals in_the_way &&
 	(
 		cd numerals_in_the_way &&
@@ -132,26 +132,13 @@ test_expect_merge_algorithm failure success 'present-despite-SKIP_WORKTREE handl
 
 		test_must_fail git merge -s recursive B^0 &&
 
-		git ls-files -t >index_files &&
-		test_cmp expected-index index_files &&
+		test_path_is_missing .git/MERGE_HEAD &&
 
-		test_path_is_file README &&
 		test_path_is_file numerals &&
 
-		test_cmp expected-merge numerals &&
-
-		# There should still be a file with "foobar" in it
-		grep foobar * &&
-
-		# 5 other files:
-		#   * expected-merge
-		#   * expected-index
-		#   * index_files
-		#   * others
-		#   * whatever name was given to the numerals file that had
-		#     "foobar" in it
-		git ls-files -o >others &&
-		test_line_count = 5 others
+		# numerals should still have "foobar" in it
+		echo foobar >expect &&
+		test_cmp expect numerals
 	)
 '
 
diff --git a/t/t7012-skip-worktree-writing.sh b/t/t7012-skip-worktree-writing.sh
index a1080b94e38..cb9f1a6981e 100755
--- a/t/t7012-skip-worktree-writing.sh
+++ b/t/t7012-skip-worktree-writing.sh
@@ -171,50 +171,20 @@ test_expect_success 'stash restore in sparse checkout' '
 
 		# Put a file in the working directory in the way
 		echo in the way >modified &&
-		git stash apply &&
+		test_must_fail git stash apply 2>error&&
 
-		# Ensure stash vivifies modifies paths...
-		cat >expect <<-EOF &&
-		H addme
-		H modified
-		H removeme
-		H subdir/A
-		S untouched
-		EOF
-		git ls-files -t >actual &&
-		test_cmp expect actual &&
+		grep "changes.*would be overwritten by merge" error &&
 
-		# ...and that the paths show up in status as changed...
-		cat >expect <<-EOF &&
-		A  addme
-		 M modified
-		 D removeme
-		 M subdir/A
-		?? actual
-		?? expect
-		?? modified.stash.XXXXXX
-		EOF
-		git status --porcelain | \
-			sed -e s/stash......./stash.XXXXXX/ >actual &&
-		test_cmp expect actual &&
+		echo in the way >expect &&
+		test_cmp expect modified &&
+		git diff --quiet HEAD ":!modified" &&
 
 		# ...and that working directory reflects the files correctly
-		test_path_is_file    addme &&
+		test_path_is_missing addme &&
 		test_path_is_file    modified &&
 		test_path_is_missing removeme &&
 		test_path_is_file    subdir/A &&
-		test_path_is_missing untouched &&
-
-		# ...including that we have the expected "modified" file...
-		cat >expect <<-EOF &&
-		modified
-		tweaked
-		EOF
-		test_cmp expect modified &&
-
-		# ...and that the other "modified" file is still present...
-		echo in the way >expect &&
-		test_cmp expect modified.stash.*
+		test_path_is_missing untouched
 	)
 '
 
diff --git a/t/t7817-grep-sparse-checkout.sh b/t/t7817-grep-sparse-checkout.sh
index 590b99bbb6f..eb595645657 100755
--- a/t/t7817-grep-sparse-checkout.sh
+++ b/t/t7817-grep-sparse-checkout.sh
@@ -83,10 +83,13 @@ test_expect_success 'setup' '
 
 # The test below covers a special case: the sparsity patterns exclude '/b' and
 # sparse checkout is enabled, but the path exists in the working tree (e.g.
-# manually created after `git sparse-checkout init`). git grep should skip it.
+# manually created after `git sparse-checkout init`).  Although b is marked
+# as SKIP_WORKTREE, git grep should notice it IS present in the worktree and
+# report it.
 test_expect_success 'working tree grep honors sparse checkout' '
 	cat >expect <<-EOF &&
 	a:text
+	b:new-text
 	EOF
 	test_when_finished "rm -f b" &&
 	echo "new-text" >b &&
@@ -126,12 +129,16 @@ test_expect_success 'grep --cached searches entries with the SKIP_WORKTREE bit'
 '
 
 # Note that sub2/ is present in the worktree but it is excluded by the sparsity
-# patterns, so grep should not recurse into it.
+# patterns.  We also explicitly mark it as SKIP_WORKTREE in case it got cleared
+# by previous git commands.  Thus sub2 starts as SKIP_WORKTREE but since it is
+# present in the working tree, grep should recurse into it.
 test_expect_success 'grep --recurse-submodules honors sparse checkout in submodule' '
 	cat >expect <<-EOF &&
 	a:text
 	sub/B/b:text
+	sub2/a:text
 	EOF
+	git update-index --skip-worktree sub2 &&
 	git grep --recurse-submodules "text" >actual &&
 	test_cmp expect actual
 '
diff --git a/unpack-trees.c b/unpack-trees.c
index 360844bda3a..96525d2ec26 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -2065,7 +2065,9 @@ static int verify_uptodate_1(const struct cache_entry *ce,
 int verify_uptodate(const struct cache_entry *ce,
 		    struct unpack_trees_options *o)
 {
-	if (!o->skip_sparse_checkout && (ce->ce_flags & CE_NEW_SKIP_WORKTREE))
+	if (!o->skip_sparse_checkout &&
+	    (ce->ce_flags & CE_SKIP_WORKTREE) &&
+	    (ce->ce_flags & CE_NEW_SKIP_WORKTREE))
 		return 0;
 	return verify_uptodate_1(ce, o, ERROR_NOT_UPTODATE_FILE);
 }