26 files changed, 498 insertions, 96 deletions
diff --git a/builtin/add.c b/builtin/add.c
index ea762a41e3..58ee3f954e 100644
--- a/builtin/add.c
+++ b/builtin/add.c
@@ -46,6 +46,9 @@ static int chmod_pathspec(struct pathspec *pathspec, char flip, int show_only)
 		struct cache_entry *ce = active_cache[i];
 		int err;
 
+		if (ce_skip_worktree(ce))
+			continue;
+
 		if (pathspec && !ce_path_match(&the_index, ce, pathspec, NULL))
 			continue;
 
@@ -141,9 +144,13 @@ static int renormalize_tracked_files(const struct pathspec *pathspec, int flags)
 {
 	int i, retval = 0;
 
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (i = 0; i < active_nr; i++) {
 		struct cache_entry *ce = active_cache[i];
 
+		if (ce_skip_worktree(ce))
+			continue;
 		if (ce_stage(ce))
 			continue; /* do not touch unmerged paths */
 		if (!S_ISREG(ce->ce_mode) && !S_ISLNK(ce->ce_mode))
@@ -172,24 +179,44 @@ static char *prune_directory(struct dir_struct *dir, struct pathspec *pathspec,
 			*dst++ = entry;
 	}
 	dir->nr = dst - dir->entries;
-	add_pathspec_matches_against_index(pathspec, &the_index, seen);
+	add_pathspec_matches_against_index(pathspec, &the_index, seen,
+					   PS_IGNORE_SKIP_WORKTREE);
 	return seen;
 }
 
-static void refresh(int verbose, const struct pathspec *pathspec)
+static int refresh(int verbose, const struct pathspec *pathspec)
 {
 	char *seen;
-	int i;
+	int i, ret = 0;
+	char *skip_worktree_seen = NULL;
+	struct string_list only_match_skip_worktree = STRING_LIST_INIT_NODUP;
+	int flags = REFRESH_IGNORE_SKIP_WORKTREE |
+		    (verbose ? REFRESH_IN_PORCELAIN : REFRESH_QUIET);
 
 	seen = xcalloc(pathspec->nr, 1);
-	refresh_index(&the_index, verbose ? REFRESH_IN_PORCELAIN : REFRESH_QUIET,
-		      pathspec, seen, _("Unstaged changes after refreshing the index:"));
+	refresh_index(&the_index, flags, pathspec, seen,
+		      _("Unstaged changes after refreshing the index:"));
 	for (i = 0; i < pathspec->nr; i++) {
-		if (!seen[i])
-			die(_("pathspec '%s' did not match any files"),
-			    pathspec->items[i].match);
+		if (!seen[i]) {
+			if (matches_skip_worktree(pathspec, i, &skip_worktree_seen)) {
+				string_list_append(&only_match_skip_worktree,
+						   pathspec->items[i].original);
+			} else {
+				die(_("pathspec '%s' did not match any files"),
+				    pathspec->items[i].original);
+			}
+		}
+	}
+
+	if (only_match_skip_worktree.nr) {
+		advise_on_updating_sparse_paths(&only_match_skip_worktree);
+		ret = 1;
 	}
+
 	free(seen);
+	free(skip_worktree_seen);
+	string_list_clear(&only_match_skip_worktree, 0);
+	return ret;
 }
 
 int run_add_interactive(const char *revision, const char *patch_mode,
@@ -565,15 +592,18 @@ int cmd_add(int argc, const char **argv, const char *prefix)
 	}
 
 	if (refresh_only) {
-		refresh(verbose, &pathspec);
+		exit_status |= refresh(verbose, &pathspec);
 		goto finish;
 	}
 
 	if (pathspec.nr) {
 		int i;
+		char *skip_worktree_seen = NULL;
+		struct string_list only_match_skip_worktree = STRING_LIST_INIT_NODUP;
 
 		if (!seen)
-			seen = find_pathspecs_matching_against_index(&pathspec, &the_index);
+			seen = find_pathspecs_matching_against_index(&pathspec,
+					&the_index, PS_IGNORE_SKIP_WORKTREE);
 
 		/*
 		 * file_exists() assumes exact match
@@ -587,12 +617,24 @@ int cmd_add(int argc, const char **argv, const char *prefix)
 
 		for (i = 0; i < pathspec.nr; i++) {
 			const char *path = pathspec.items[i].match;
+
 			if (pathspec.items[i].magic & PATHSPEC_EXCLUDE)
 				continue;
-			if (!seen[i] && path[0] &&
-			    ((pathspec.items[i].magic &
-			      (PATHSPEC_GLOB | PATHSPEC_ICASE)) ||
-			     !file_exists(path))) {
+			if (seen[i])
+				continue;
+
+			if (matches_skip_worktree(&pathspec, i, &skip_worktree_seen)) {
+				string_list_append(&only_match_skip_worktree,
+						   pathspec.items[i].original);
+				continue;
+			}
+
+			/* Don't complain at 'git add .' on empty repo */
+			if (!path[0])
+				continue;
+
+			if ((pathspec.items[i].magic & (PATHSPEC_GLOB | PATHSPEC_ICASE)) ||
+			    !file_exists(path)) {
 				if (ignore_missing) {
 					int dtype = DT_UNKNOWN;
 					if (is_excluded(&dir, &the_index, path, &dtype))
@@ -603,7 +645,16 @@ int cmd_add(int argc, const char **argv, const char *prefix)
 					    pathspec.items[i].original);
 			}
 		}
+
+
+		if (only_match_skip_worktree.nr) {
+			advise_on_updating_sparse_paths(&only_match_skip_worktree);
+			exit_status = 1;
+		}
+
 		free(seen);
+		free(skip_worktree_seen);
+		string_list_clear(&only_match_skip_worktree, 0);
 	}
 
 	plug_bulk_checkin();
diff --git a/builtin/branch.c b/builtin/branch.c
index bcc00bcf18..b23b1d1752 100644
--- a/builtin/branch.c
+++ b/builtin/branch.c
@@ -411,6 +411,8 @@ static void print_ref_list(struct ref_filter *filter, struct ref_sorting *sortin
 {
 	int i;
 	struct ref_array array;
+	struct strbuf out = STRBUF_INIT;
+	struct strbuf err = STRBUF_INIT;
 	int maxwidth = 0;
 	const char *remote_prefix = "";
 	char *to_free = NULL;
@@ -440,8 +442,8 @@ static void print_ref_list(struct ref_filter *filter, struct ref_sorting *sortin
 	ref_array_sort(sorting, &array);
 
 	for (i = 0; i < array.nr; i++) {
-		struct strbuf out = STRBUF_INIT;
-		struct strbuf err = STRBUF_INIT;
+		strbuf_reset(&err);
+		strbuf_reset(&out);
 		if (format_ref_array_item(array.items[i], format, &out, &err))
 			die("%s", err.buf);
 		if (column_active(colopts)) {
@@ -452,10 +454,10 @@ static void print_ref_list(struct ref_filter *filter, struct ref_sorting *sortin
 			fwrite(out.buf, 1, out.len, stdout);
 			putchar('\n');
 		}
-		strbuf_release(&err);
-		strbuf_release(&out);
 	}
 
+	strbuf_release(&err);
+	strbuf_release(&out);
 	ref_array_clear(&array);
 	free(to_free);
 }
diff --git a/builtin/bugreport.c b/builtin/bugreport.c
index ad3cc9c02f..9915a5841d 100644
--- a/builtin/bugreport.c
+++ b/builtin/bugreport.c
@@ -129,6 +129,7 @@ int cmd_bugreport(int argc, const char **argv, const char *prefix)
 	char *option_output = NULL;
 	char *option_suffix = "%Y-%m-%d-%H%M";
 	const char *user_relative_path = NULL;
+	char *prefixed_filename;
 
 	const struct option bugreport_options[] = {
 		OPT_STRING('o', "output-directory", &option_output, N_("path"),
@@ -142,9 +143,9 @@ int cmd_bugreport(int argc, const char **argv, const char *prefix)
 			     bugreport_usage, 0);
 
 	/* Prepare the path to put the result */
-	strbuf_addstr(&report_path,
-		      prefix_filename(prefix,
-				      option_output ? option_output : ""));
+	prefixed_filename = prefix_filename(prefix,
+					    option_output ? option_output : "");
+	strbuf_addstr(&report_path, prefixed_filename);
 	strbuf_complete(&report_path, '/');
 
 	strbuf_addstr(&report_path, "git-bugreport-");
@@ -189,6 +190,7 @@ int cmd_bugreport(int argc, const char **argv, const char *prefix)
 	fprintf(stderr, _("Created new report at '%s'.\n"),
 		user_relative_path);
 
+	free(prefixed_filename);
 	UNLEAK(buffer);
 	UNLEAK(report_path);
 	return !!launch_editor(report_path.buf, NULL, NULL);
diff --git a/builtin/check-ignore.c b/builtin/check-ignore.c
index 3c652748d5..81234552b7 100644
--- a/builtin/check-ignore.c
+++ b/builtin/check-ignore.c
@@ -100,7 +100,8 @@ static int check_ignore(struct dir_struct *dir,
 	 * should not be ignored, in order to be consistent with
 	 * 'git status', 'git add' etc.
 	 */
-	seen = find_pathspecs_matching_against_index(&pathspec, &the_index);
+	seen = find_pathspecs_matching_against_index(&pathspec, &the_index,
+						     PS_HEED_SKIP_WORKTREE);
 	for (i = 0; i < pathspec.nr; i++) {
 		full_path = pathspec.items[i].match;
 		pattern = NULL;
@@ -118,6 +119,7 @@ static int check_ignore(struct dir_struct *dir,
 			num_ignored++;
 	}
 	free(seen);
+	clear_pathspec(&pathspec);
 
 	return num_ignored;
 }
diff --git a/builtin/checkout--worker.c b/builtin/checkout--worker.c
new file mode 100644
index 0000000000..31e0de2f7e
--- /dev/null
+++ b/builtin/checkout--worker.c
@@ -0,0 +1,145 @@
+#include "builtin.h"
+#include "config.h"
+#include "entry.h"
+#include "parallel-checkout.h"
+#include "parse-options.h"
+#include "pkt-line.h"
+
+static void packet_to_pc_item(const char *buffer, int len,
+			      struct parallel_checkout_item *pc_item)
+{
+	const struct pc_item_fixed_portion *fixed_portion;
+	const char *variant;
+	char *encoding;
+
+	if (len < sizeof(struct pc_item_fixed_portion))
+		BUG("checkout worker received too short item (got %dB, exp %dB)",
+		    len, (int)sizeof(struct pc_item_fixed_portion));
+
+	fixed_portion = (struct pc_item_fixed_portion *)buffer;
+
+	if (len - sizeof(struct pc_item_fixed_portion) !=
+		fixed_portion->name_len + fixed_portion->working_tree_encoding_len)
+		BUG("checkout worker received corrupted item");
+
+	variant = buffer + sizeof(struct pc_item_fixed_portion);
+
+	/*
+	 * Note: the main process uses zero length to communicate that the
+	 * encoding is NULL. There is no use case that requires sending an
+	 * actual empty string, since convert_attrs() never sets
+	 * ca.working_tree_enconding to "".
+	 */
+	if (fixed_portion->working_tree_encoding_len) {
+		encoding = xmemdupz(variant,
+				    fixed_portion->working_tree_encoding_len);
+		variant += fixed_portion->working_tree_encoding_len;
+	} else {
+		encoding = NULL;
+	}
+
+	memset(pc_item, 0, sizeof(*pc_item));
+	pc_item->ce = make_empty_transient_cache_entry(fixed_portion->name_len);
+	pc_item->ce->ce_namelen = fixed_portion->name_len;
+	pc_item->ce->ce_mode = fixed_portion->ce_mode;
+	memcpy(pc_item->ce->name, variant, pc_item->ce->ce_namelen);
+	oidcpy(&pc_item->ce->oid, &fixed_portion->oid);
+
+	pc_item->id = fixed_portion->id;
+	pc_item->ca.crlf_action = fixed_portion->crlf_action;
+	pc_item->ca.ident = fixed_portion->ident;
+	pc_item->ca.working_tree_encoding = encoding;
+}
+
+static void report_result(struct parallel_checkout_item *pc_item)
+{
+	struct pc_item_result res;
+	size_t size;
+
+	res.id = pc_item->id;
+	res.status = pc_item->status;
+
+	if (pc_item->status == PC_ITEM_WRITTEN) {
+		res.st = pc_item->st;
+		size = sizeof(res);
+	} else {
+		size = PC_ITEM_RESULT_BASE_SIZE;
+	}
+
+	packet_write(1, (const char *)&res, size);
+}
+
+/* Free the worker-side malloced data, but not pc_item itself. */
+static void release_pc_item_data(struct parallel_checkout_item *pc_item)
+{
+	free((char *)pc_item->ca.working_tree_encoding);
+	discard_cache_entry(pc_item->ce);
+}
+
+static void worker_loop(struct checkout *state)
+{
+	struct parallel_checkout_item *items = NULL;
+	size_t i, nr = 0, alloc = 0;
+
+	while (1) {
+		int len = packet_read(0, NULL, NULL, packet_buffer,
+				      sizeof(packet_buffer), 0);
+
+		if (len < 0)
+			BUG("packet_read() returned negative value");
+		else if (!len)
+			break;
+
+		ALLOC_GROW(items, nr + 1, alloc);
+		packet_to_pc_item(packet_buffer, len, &items[nr++]);
+	}
+
+	for (i = 0; i < nr; i++) {
+		struct parallel_checkout_item *pc_item = &items[i];
+		write_pc_item(pc_item, state);
+		report_result(pc_item);
+		release_pc_item_data(pc_item);
+	}
+
+	packet_flush(1);
+
+	free(items);
+}
+
+static const char * const checkout_worker_usage[] = {
+	N_("git checkout--worker [<options>]"),
+	NULL
+};
+
+int cmd_checkout__worker(int argc, const char **argv, const char *prefix)
+{
+	struct checkout state = CHECKOUT_INIT;
+	struct option checkout_worker_options[] = {
+		OPT_STRING(0, "prefix", &state.base_dir, N_("string"),
+			N_("when creating files, prepend <string>")),
+		OPT_END()
+	};
+
+	if (argc == 2 && !strcmp(argv[1], "-h"))
+		usage_with_options(checkout_worker_usage,
+				   checkout_worker_options);
+
+	git_config(git_default_config, NULL);
+	argc = parse_options(argc, argv, prefix, checkout_worker_options,
+			     checkout_worker_usage, 0);
+	if (argc > 0)
+		usage_with_options(checkout_worker_usage, checkout_worker_options);
+
+	if (state.base_dir)
+		state.base_dir_len = strlen(state.base_dir);
+
+	/*
+	 * Setting this on a worker won't actually update the index. We just
+	 * need to tell the checkout machinery to lstat() the written entries,
+	 * so that we can send this data back to the main process.
+	 */
+	state.refresh_cache = 1;
+
+	worker_loop(&state);
+	return 0;
+}
diff --git a/builtin/checkout-index.c b/builtin/checkout-index.c
index c0bf4ac1b2..c9a3c71914 100644
--- a/builtin/checkout-index.c
+++ b/builtin/checkout-index.c
@@ -120,6 +120,8 @@ static void checkout_all(const char *prefix, int prefix_length)
 	int i, errs = 0;
 	struct cache_entry *last_ce = NULL;
 
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (i = 0; i < active_nr ; i++) {
 		struct cache_entry *ce = active_cache[i];
 		if (ce_stage(ce) != checkout_stage
diff --git a/builtin/checkout.c b/builtin/checkout.c
index 8a12b92c5f..0bf61e6eef 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -369,6 +369,9 @@ static int checkout_worktree(const struct checkout_opts *opts,
 			       NULL);
 
 	enable_delayed_checkout(&state);
+
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (pos = 0; pos < active_nr; pos++) {
 		struct cache_entry *ce = active_cache[pos];
 		if (ce->ce_flags & CE_MATCHED) {
@@ -513,6 +516,8 @@ static int checkout_paths(const struct checkout_opts *opts,
 	 * Make sure all pathspecs participated in locating the paths
 	 * to be checked out.
 	 */
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (pos = 0; pos < active_nr; pos++)
 		if (opts->overlay_mode)
 			mark_ce_for_checkout_overlay(active_cache[pos],
@@ -602,6 +607,7 @@ static void show_local_changes(struct object *head,
 	diff_setup_done(&rev.diffopt);
 	add_pending_object(&rev, head, NULL);
 	run_diff_index(&rev, 0);
+	object_array_clear(&rev.pending);
 }
 
 static void describe_detached_head(const char *msg, struct commit *commit)
diff --git a/builtin/commit.c b/builtin/commit.c
index 55d50a8891..190d215d43 100644
--- a/builtin/commit.c
+++ b/builtin/commit.c
@@ -261,6 +261,8 @@ static int list_paths(struct string_list *list, const char *with_tree,
 		free(max_prefix);
 	}
 
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (i = 0; i < active_nr; i++) {
 		const struct cache_entry *ce = active_cache[i];
 		struct string_list_item *item;
@@ -976,6 +978,8 @@ static int prepare_to_commit(const char *index_file, const char *prefix,
 		if (get_oid(parent, &oid)) {
 			int i, ita_nr = 0;
 
+			/* TODO: audit for interaction with sparse-index. */
+			ensure_full_index(&the_index);
 			for (i = 0; i < active_nr; i++)
 				if (ce_intent_to_add(active_cache[i]))
 					ita_nr++;
diff --git a/builtin/config.c b/builtin/config.c
index f71fa39b38..865fddd6ce 100644
--- a/builtin/config.c
+++ b/builtin/config.c
@@ -671,9 +671,9 @@ int cmd_config(int argc, const char **argv, const char *prefix)
 	}
 
 	if (use_global_config) {
-		char *user_config = expand_user_path("~/.gitconfig", 0);
-		char *xdg_config = xdg_config_home("config");
+		char *user_config, *xdg_config;
 
+		git_global_config(&user_config, &xdg_config);
 		if (!user_config)
 			/*
 			 * It is unknown if HOME/.gitconfig exists, so
@@ -695,7 +695,7 @@ int cmd_config(int argc, const char **argv, const char *prefix)
 		}
 	}
 	else if (use_system_config) {
-		given_config_source.file = git_etc_gitconfig();
+		given_config_source.file = git_system_config();
 		given_config_source.scope = CONFIG_SCOPE_SYSTEM;
 	} else if (use_local_config) {
 		given_config_source.file = git_pathdup("config");
diff --git a/builtin/difftool.c b/builtin/difftool.c
index ef25729d49..0202a43052 100644
--- a/builtin/difftool.c
+++ b/builtin/difftool.c
@@ -585,6 +585,9 @@ static int run_dir_diff(const char *extcmd, int symlinks, const char *prefix,
 		setenv("GIT_DIFFTOOL_DIRDIFF", "true", 1);
 	rc = run_command_v_opt(helper_argv, flags);
 
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&wtindex);
+
 	/*
 	 * If the diff includes working copy files and those
 	 * files were modified during the diff, then the changes
diff --git a/builtin/fetch.c b/builtin/fetch.c
index 0b90de87c7..97c4fe6e6d 100644
--- a/builtin/fetch.c
+++ b/builtin/fetch.c
@@ -48,6 +48,7 @@ enum {
 static int fetch_prune_config = -1; /* unspecified */
 static int fetch_show_forced_updates = 1;
 static uint64_t forced_updates_ms = 0;
+static int prefetch = 0;
 static int prune = -1; /* unspecified */
 #define PRUNE_BY_DEFAULT 0 /* do we prune by default? */
 
@@ -158,6 +159,8 @@ static struct option builtin_fetch_options[] = {
 		    N_("do not fetch all tags (--no-tags)"), TAGS_UNSET),
 	OPT_INTEGER('j', "jobs", &max_jobs,
 		    N_("number of submodules fetched in parallel")),
+	OPT_BOOL(0, "prefetch", &prefetch,
+		 N_("modify the refspec to place all refs within refs/prefetch/")),
 	OPT_BOOL('p', "prune", &prune,
 		 N_("prune remote-tracking branches no longer on remote")),
 	OPT_BOOL('P', "prune-tags", &prune_tags,
@@ -436,6 +439,56 @@ static void find_non_local_tags(const struct ref *refs,
 	oidset_clear(&fetch_oids);
 }
 
+static void filter_prefetch_refspec(struct refspec *rs)
+{
+	int i;
+
+	if (!prefetch)
+		return;
+
+	for (i = 0; i < rs->nr; i++) {
+		struct strbuf new_dst = STRBUF_INIT;
+		char *old_dst;
+		const char *sub = NULL;
+
+		if (rs->items[i].negative)
+			continue;
+		if (!rs->items[i].dst ||
+		    (rs->items[i].src &&
+		     !strncmp(rs->items[i].src, "refs/tags/", 10))) {
+			int j;
+
+			free(rs->items[i].src);
+			free(rs->items[i].dst);
+
+			for (j = i + 1; j < rs->nr; j++) {
+				rs->items[j - 1] = rs->items[j];
+				rs->raw[j - 1] = rs->raw[j];
+			}
+			rs->nr--;
+			i--;
+			continue;
+		}
+
+		old_dst = rs->items[i].dst;
+		strbuf_addstr(&new_dst, "refs/prefetch/");
+
+		/*
+		 * If old_dst starts with "refs/", then place
+		 * sub after that prefix. Otherwise, start at
+		 * the beginning of the string.
+		 */
+		if (!skip_prefix(old_dst, "refs/", &sub))
+			sub = old_dst;
+		strbuf_addstr(&new_dst, sub);
+
+		rs->items[i].dst = strbuf_detach(&new_dst, NULL);
+		rs->items[i].force = 1;
+
+		free(old_dst);
+	}
+}
+
 static struct ref *get_ref_map(struct remote *remote,
 			       const struct ref *remote_refs,
 			       struct refspec *rs,
@@ -452,6 +505,10 @@ static struct ref *get_ref_map(struct remote *remote,
 	struct hashmap existing_refs;
 	int existing_refs_populated = 0;
 
+	filter_prefetch_refspec(rs);
+	if (remote)
+		filter_prefetch_refspec(&remote->fetch);
+
 	if (rs->nr) {
 		struct refspec *fetch_refspec;
 
@@ -520,7 +577,7 @@ static struct ref *get_ref_map(struct remote *remote,
 			if (has_merge &&
 			    !strcmp(branch->remote_name, remote->name))
 				add_merge_config(&ref_map, remote_refs, branch, &tail);
-		} else {
+		} else if (!prefetch) {
 			ref_map = get_remote_ref(remote_refs, "HEAD");
 			if (!ref_map)
 				die(_("Couldn't find remote ref HEAD"));
diff --git a/builtin/for-each-ref.c b/builtin/for-each-ref.c
index cb9c81a046..89cb6307d4 100644
--- a/builtin/for-each-ref.c
+++ b/builtin/for-each-ref.c
@@ -22,6 +22,8 @@ int cmd_for_each_ref(int argc, const char **argv, const char *prefix)
 	struct ref_array array;
 	struct ref_filter filter;
 	struct ref_format format = REF_FORMAT_INIT;
+	struct strbuf output = STRBUF_INIT;
+	struct strbuf err = STRBUF_INIT;
 
 	struct option opts[] = {
 		OPT_BIT('s', "shell", &format.quote_style,
@@ -80,8 +82,20 @@ int cmd_for_each_ref(int argc, const char **argv, const char *prefix)
 
 	if (!maxcount || array.nr < maxcount)
 		maxcount = array.nr;
-	for (i = 0; i < maxcount; i++)
-		show_ref_array_item(array.items[i], &format);
+	for (i = 0; i < maxcount; i++) {
+		strbuf_reset(&err);
+		strbuf_reset(&output);
+		if (format_ref_array_item(array.items[i], &format, &output, &err))
+			die("%s", err.buf);
+		fwrite(output.buf, 1, output.len, stdout);
+		putchar('\n');
+	}
+
+	strbuf_release(&err);
+	strbuf_release(&output);
 	ref_array_clear(&array);
+	free_commit_list(filter.with_commit);
+	free_commit_list(filter.no_commit);
+	UNLEAK(sorting);
 	return 0;
 }
diff --git a/builtin/fsck.c b/builtin/fsck.c
index 70ff95837a..87a99b0108 100644
--- a/builtin/fsck.c
+++ b/builtin/fsck.c
@@ -725,7 +725,7 @@ static int fsck_cache_tree(struct cache_tree *it)
 
 static void mark_object_for_connectivity(const struct object_id *oid)
 {
-	struct object *obj = lookup_unknown_object(oid);
+	struct object *obj = lookup_unknown_object(the_repository, oid);
 	obj->flags |= HAS_OBJ;
 }
 
@@ -881,6 +881,8 @@ int cmd_fsck(int argc, const char **argv, const char *prefix)
 		verify_index_checksum = 1;
 		verify_ce_order = 1;
 		read_cache();
+		/* TODO: audit for interaction with sparse-index. */
+		ensure_full_index(&the_index);
 		for (i = 0; i < active_nr; i++) {
 			unsigned int mode;
 			struct blob *blob;
diff --git a/builtin/gc.c b/builtin/gc.c
index ef7226d7bc..98a803196b 100644
--- a/builtin/gc.c
+++ b/builtin/gc.c
@@ -873,55 +873,40 @@ static int maintenance_task_commit_graph(struct maintenance_run_opts *opts)
 	return 0;
 }
 
-static int fetch_remote(const char *remote, struct maintenance_run_opts *opts)
+static int fetch_remote(struct remote *remote, void *cbdata)
 {
+	struct maintenance_run_opts *opts = cbdata;
 	struct child_process child = CHILD_PROCESS_INIT;
 
+	if (remote->skip_default_update)
+		return 0;
+
 	child.git_cmd = 1;
-	strvec_pushl(&child.args, "fetch", remote, "--prune", "--no-tags",
+	strvec_pushl(&child.args, "fetch", remote->name,
+		     "--prefetch", "--prune", "--no-tags",
 		     "--no-write-fetch-head", "--recurse-submodules=no",
-		     "--refmap=", NULL);
+		     NULL);
 
 	if (opts->quiet)
 		strvec_push(&child.args, "--quiet");
 
-	strvec_pushf(&child.args, "+refs/heads/*:refs/prefetch/%s/*", remote);
-
 	return !!run_command(&child);
 }
 
-static int append_remote(struct remote *remote, void *cbdata)
-{
-	struct string_list *remotes = (struct string_list *)cbdata;
-
-	string_list_append(remotes, remote->name);
-	return 0;
-}
-
 static int maintenance_task_prefetch(struct maintenance_run_opts *opts)
 {
-	int result = 0;
-	struct string_list_item *item;
-	struct string_list remotes = STRING_LIST_INIT_DUP;
-
 	git_config_set_multivar_gently("log.excludedecoration",
 					"refs/prefetch/",
 					"refs/prefetch/",
 					CONFIG_FLAGS_FIXED_VALUE |
 					CONFIG_FLAGS_MULTI_REPLACE);
 
-	if (for_each_remote(append_remote, &remotes)) {
-		error(_("failed to fill remotes"));
-		result = 1;
-		goto cleanup;
+	if (for_each_remote(fetch_remote, opts)) {
+		error(_("failed to prefetch remotes"));
+		return 1;
 	}
 
-	for_each_string_list_item(item, &remotes)
-		result |= fetch_remote(item->string, opts);
-
-cleanup:
-	string_list_clear(&remotes, 0);
-	return result;
+	return 0;
 }
 
 static int maintenance_task_gc(struct maintenance_run_opts *opts)
diff --git a/builtin/grep.c b/builtin/grep.c
index e0e326004e..ab8822e68f 100644
--- a/builtin/grep.c
+++ b/builtin/grep.c
@@ -504,6 +504,8 @@ static int grep_cache(struct grep_opt *opt,
 	if (repo_read_index(repo) < 0)
 		die(_("index file corrupt"));
 
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(repo->index);
 	for (nr = 0; nr < repo->index->cache_nr; nr++) {
 		const struct cache_entry *ce = repo->index->cache[nr];
 
diff --git a/builtin/log.c b/builtin/log.c
index 8acd285daf..6102893fcc 100644
--- a/builtin/log.c
+++ b/builtin/log.c
@@ -481,6 +481,8 @@ static int git_log_config(const char *var, const char *value, void *cb)
 			decoration_style = 0; /* maybe warn? */
 		return 0;
 	}
+	if (!strcmp(var, "log.diffmerges"))
+		return diff_merges_config(value);
 	if (!strcmp(var, "log.showroot")) {
 		default_show_root = git_config_bool(var, value);
 		return 0;
diff --git a/builtin/ls-files.c b/builtin/ls-files.c
index c589eb7f89..844c7f4e0e 100644
--- a/builtin/ls-files.c
+++ b/builtin/ls-files.c
@@ -57,7 +57,7 @@ static const char *tag_modified = "";
 static const char *tag_skip_worktree = "";
 static const char *tag_resolve_undo = "";
 
-static void write_eolinfo(const struct index_state *istate,
+static void write_eolinfo(struct index_state *istate,
 			  const struct cache_entry *ce, const char *path)
 {
 	if (show_eol) {
@@ -122,7 +122,7 @@ static void print_debug(const struct cache_entry *ce)
 	}
 }
 
-static void show_dir_entry(const struct index_state *istate,
+static void show_dir_entry(struct index_state *istate,
 			   const char *tag, struct dir_entry *ent)
 {
 	int len = max_prefix_len;
@@ -139,7 +139,7 @@ static void show_dir_entry(const struct index_state *istate,
 	write_name(ent->name);
 }
 
-static void show_other_files(const struct index_state *istate,
+static void show_other_files(struct index_state *istate,
 			     const struct dir_struct *dir)
 {
 	int i;
@@ -152,7 +152,7 @@ static void show_other_files(const struct index_state *istate,
 	}
 }
 
-static void show_killed_files(const struct index_state *istate,
+static void show_killed_files(struct index_state *istate,
 			      const struct dir_struct *dir)
 {
 	int i;
@@ -254,7 +254,7 @@ static void show_ce(struct repository *repo, struct dir_struct *dir,
 	}
 }
 
-static void show_ru_info(const struct index_state *istate)
+static void show_ru_info(struct index_state *istate)
 {
 	struct string_list_item *item;
 
@@ -317,6 +317,8 @@ static void show_files(struct repository *repo, struct dir_struct *dir)
 
 	if (!(show_cached || show_stage || show_deleted || show_modified))
 		return;
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(repo->index);
 	for (i = 0; i < repo->index->cache_nr; i++) {
 		const struct cache_entry *ce = repo->index->cache[i];
 		struct stat st;
@@ -494,6 +496,8 @@ void overlay_tree_on_index(struct index_state *istate,
 		die("bad tree-ish %s", tree_name);
 
 	/* Hoist the unmerged entries up to stage #3 to make room */
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(istate);
 	for (i = 0; i < istate->cache_nr; i++) {
 		struct cache_entry *ce = istate->cache[i];
 		if (!ce_stage(ce))
@@ -603,7 +607,7 @@ static int option_parse_exclude_standard(const struct option *opt,
 int cmd_ls_files(int argc, const char **argv, const char *cmd_prefix)
 {
 	int require_work_tree = 0, show_tag = 0, i;
-	const char *max_prefix;
+	char *max_prefix;
 	struct dir_struct dir;
 	struct pattern_list *pl;
 	struct string_list exclude_list = STRING_LIST_INIT_NODUP;
@@ -781,5 +785,6 @@ int cmd_ls_files(int argc, const char **argv, const char *cmd_prefix)
 	}
 
 	dir_clear(&dir);
+	free(max_prefix);
 	return 0;
 }
diff --git a/builtin/merge-index.c b/builtin/merge-index.c
index 38ea6ad6ca..c0383fe9df 100644
--- a/builtin/merge-index.c
+++ b/builtin/merge-index.c
@@ -58,6 +58,8 @@ static void merge_one_path(const char *path)
 static void merge_all(void)
 {
 	int i;
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (i = 0; i < active_nr; i++) {
 		const struct cache_entry *ce = active_cache[i];
 		if (!ce_stage(ce))
@@ -80,6 +82,9 @@ int cmd_merge_index(int argc, const char **argv, const char *prefix)
 
 	read_cache();
 
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
+
 	i = 1;
 	if (!strcmp(argv[i], "-o")) {
 		one_shot = 1;
diff --git a/builtin/pack-objects.c b/builtin/pack-objects.c
index 5b25382204..14bf70092d 100644
--- a/builtin/pack-objects.c
+++ b/builtin/pack-objects.c
@@ -3386,7 +3386,7 @@ static void add_objects_in_unpacked_packs(void)
 
 		for (i = 0; i < p->num_objects; i++) {
 			nth_packed_object_id(&oid, p, i);
-			o = lookup_unknown_object(&oid);
+			o = lookup_unknown_object(the_repository, &oid);
 			if (!(o->flags & OBJECT_ADDED))
 				mark_in_pack_object(o, p, &in_pack);
 			o->flags |= OBJECT_ADDED;
@@ -3516,7 +3516,7 @@ static int pack_options_allow_reuse(void)
 
 static int get_object_list_from_bitmap(struct rev_info *revs)
 {
-	if (!(bitmap_git = prepare_bitmap_walk(revs, &filter_options)))
+	if (!(bitmap_git = prepare_bitmap_walk(revs, &filter_options, 0)))
 		return -1;
 
 	if (pack_options_allow_reuse() &&
@@ -3527,7 +3527,8 @@ static int get_object_list_from_bitmap(struct rev_info *revs)
 			&reuse_packfile_bitmap)) {
 		assert(reuse_packfile_objects);
 		nr_result += reuse_packfile_objects;
-		display_progress(progress_state, nr_result);
+		nr_seen += reuse_packfile_objects;
+		display_progress(progress_state, nr_seen);
 	}
 
 	traverse_bitmap_commit_list(bitmap_git, revs,
@@ -3547,6 +3548,37 @@ static void record_recent_commit(struct commit *commit, void *data)
 	oid_array_append(&recent_objects, &commit->object.oid);
 }
 
+static int mark_bitmap_preferred_tip(const char *refname,
+				     const struct object_id *oid, int flags,
+				     void *_data)
+{
+	struct object_id peeled;
+	struct object *object;
+
+	if (!peel_iterated_oid(oid, &peeled))
+		oid = &peeled;
+
+	object = parse_object_or_die(oid, refname);
+	if (object->type == OBJ_COMMIT)
+		object->flags |= NEEDS_BITMAP;
+
+	return 0;
+}
+
+static void mark_bitmap_preferred_tips(void)
+{
+	struct string_list_item *item;
+	const struct string_list *preferred_tips;
+
+	preferred_tips = bitmap_preferred_tips(the_repository);
+	if (!preferred_tips)
+		return;
+
+	for_each_string_list_item(item, preferred_tips) {
+		for_each_ref_in(item->string, mark_bitmap_preferred_tip, NULL);
+	}
+}
+
 static void get_object_list(int ac, const char **av)
 {
 	struct rev_info revs;
@@ -3601,6 +3633,9 @@ static void get_object_list(int ac, const char **av)
 	if (use_delta_islands)
 		load_delta_islands(the_repository, progress);
 
+	if (write_bitmap_index)
+		mark_bitmap_preferred_tips();
+
 	if (prepare_revision_walk(&revs))
 		die(_("revision walk setup failed"));
 	mark_edges_uninteresting(&revs, show_edge, sparse);
diff --git a/builtin/rebase.c b/builtin/rebase.c
index c9206b40ea..12f093121d 100644
--- a/builtin/rebase.c
+++ b/builtin/rebase.c
@@ -738,6 +738,7 @@ static int finish_rebase(struct rebase_options *opts)
 	int ret = 0;
 
 	delete_ref(NULL, "REBASE_HEAD", NULL, REF_NO_DEREF);
+	unlink(git_path_auto_merge(the_repository));
 	apply_autostash(state_dir_path("autostash", opts));
 	close_object_store(the_repository->objects);
 	/*
@@ -2108,6 +2109,7 @@ cleanup:
 	free(options.head_name);
 	free(options.gpg_sign_opt);
 	free(options.cmd);
+	strbuf_release(&options.git_format_patch_opt);
 	free(squash_onto_name);
 	return ret;
 }
diff --git a/builtin/rev-list.c b/builtin/rev-list.c
index b4d8ea0a35..7677b1af5a 100644
--- a/builtin/rev-list.c
+++ b/builtin/rev-list.c
@@ -398,7 +398,8 @@ static inline int parse_missing_action_value(const char *value)
 }
 
 static int try_bitmap_count(struct rev_info *revs,
-			    struct list_objects_filter_options *filter)
+			    struct list_objects_filter_options *filter,
+			    int filter_provided_objects)
 {
 	uint32_t commit_count = 0,
 		 tag_count = 0,
@@ -433,7 +434,7 @@ static int try_bitmap_count(struct rev_info *revs,
 	 */
 	max_count = revs->max_count;
 
-	bitmap_git = prepare_bitmap_walk(revs, filter);
+	bitmap_git = prepare_bitmap_walk(revs, filter, filter_provided_objects);
 	if (!bitmap_git)
 		return -1;
 
@@ -450,7 +451,8 @@ static int try_bitmap_count(struct rev_info *revs,
 }
 
 static int try_bitmap_traversal(struct rev_info *revs,
-				struct list_objects_filter_options *filter)
+				struct list_objects_filter_options *filter,
+				int filter_provided_objects)
 {
 	struct bitmap_index *bitmap_git;
 
@@ -461,7 +463,7 @@ static int try_bitmap_traversal(struct rev_info *revs,
 	if (revs->max_count >= 0)
 		return -1;
 
-	bitmap_git = prepare_bitmap_walk(revs, filter);
+	bitmap_git = prepare_bitmap_walk(revs, filter, filter_provided_objects);
 	if (!bitmap_git)
 		return -1;
 
@@ -471,14 +473,15 @@ static int try_bitmap_traversal(struct rev_info *revs,
 }
 
 static int try_bitmap_disk_usage(struct rev_info *revs,
-				 struct list_objects_filter_options *filter)
+				 struct list_objects_filter_options *filter,
+				 int filter_provided_objects)
 {
 	struct bitmap_index *bitmap_git;
 
 	if (!show_disk_usage)
 		return -1;
 
-	bitmap_git = prepare_bitmap_walk(revs, filter);
+	bitmap_git = prepare_bitmap_walk(revs, filter, filter_provided_objects);
 	if (!bitmap_git)
 		return -1;
 
@@ -499,6 +502,7 @@ int cmd_rev_list(int argc, const char **argv, const char *prefix)
 	int bisect_show_vars = 0;
 	int bisect_find_all = 0;
 	int use_bitmap_index = 0;
+	int filter_provided_objects = 0;
 	const char *show_progress = NULL;
 
 	if (argc == 2 && !strcmp(argv[1], "-h"))
@@ -599,6 +603,10 @@ int cmd_rev_list(int argc, const char **argv, const char *prefix)
 			list_objects_filter_set_no_filter(&filter_options);
 			continue;
 		}
+		if (!strcmp(arg, "--filter-provided-objects")) {
+			filter_provided_objects = 1;
+			continue;
+		}
 		if (!strcmp(arg, "--filter-print-omitted")) {
 			arg_print_omitted = 1;
 			continue;
@@ -665,11 +673,11 @@ int cmd_rev_list(int argc, const char **argv, const char *prefix)
 		progress = start_delayed_progress(show_progress, 0);
 
 	if (use_bitmap_index) {
-		if (!try_bitmap_count(&revs, &filter_options))
+		if (!try_bitmap_count(&revs, &filter_options, filter_provided_objects))
 			return 0;
-		if (!try_bitmap_disk_usage(&revs, &filter_options))
+		if (!try_bitmap_disk_usage(&revs, &filter_options, filter_provided_objects))
 			return 0;
-		if (!try_bitmap_traversal(&revs, &filter_options))
+		if (!try_bitmap_traversal(&revs, &filter_options, filter_provided_objects))
 			return 0;
 	}
 
@@ -694,6 +702,16 @@ int cmd_rev_list(int argc, const char **argv, const char *prefix)
 			return show_bisect_vars(&info, reaches, all);
 	}
 
+	if (filter_provided_objects) {
+		struct commit_list *c;
+		for (i = 0; i < revs.pending.nr; i++) {
+			struct object_array_entry *pending = revs.pending.objects + i;
+			pending->item->flags |= NOT_USER_GIVEN;
+		}
+		for (c = revs.commits; c; c = c->next)
+			c->item->object.flags |= NOT_USER_GIVEN;
+	}
+
 	if (arg_print_omitted)
 		oidset_init(&omitted_objects, DEFAULT_OIDSET_SIZE);
 	if (arg_missing_action == MA_PRINT)
diff --git a/builtin/rm.c b/builtin/rm.c
index 4858631e0f..8a24c715e0 100644
--- a/builtin/rm.c
+++ b/builtin/rm.c
@@ -5,6 +5,7 @@
  */
 #define USE_THE_INDEX_COMPATIBILITY_MACROS
 #include "builtin.h"
+#include "advice.h"
 #include "config.h"
 #include "lockfile.h"
 #include "dir.h"
@@ -254,7 +255,7 @@ static struct option builtin_rm_options[] = {
 int cmd_rm(int argc, const char **argv, const char *prefix)
 {
 	struct lock_file lock_file = LOCK_INIT;
-	int i;
+	int i, ret = 0;
 	struct pathspec pathspec;
 	char *seen;
 
@@ -293,8 +294,12 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 
 	seen = xcalloc(pathspec.nr, 1);
 
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (i = 0; i < active_nr; i++) {
 		const struct cache_entry *ce = active_cache[i];
+		if (ce_skip_worktree(ce))
+			continue;
 		if (!ce_path_match(&the_index, ce, &pathspec, seen))
 			continue;
 		ALLOC_GROW(list.entry, list.nr + 1, list.alloc);
@@ -308,25 +313,37 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	if (pathspec.nr) {
 		const char *original;
 		int seen_any = 0;
+		char *skip_worktree_seen = NULL;
+		struct string_list only_match_skip_worktree = STRING_LIST_INIT_NODUP;
+
 		for (i = 0; i < pathspec.nr; i++) {
 			original = pathspec.items[i].original;
-			if (!seen[i]) {
-				if (!ignore_unmatch) {
-					die(_("pathspec '%s' did not match any files"),
-					    original);
-				}
-			}
-			else {
+			if (seen[i])
 				seen_any = 1;
-			}
+			else if (ignore_unmatch)
+				continue;
+			else if (matches_skip_worktree(&pathspec, i, &skip_worktree_seen))
+				string_list_append(&only_match_skip_worktree, original);
+			else
+				die(_("pathspec '%s' did not match any files"), original);
+
 			if (!recursive && seen[i] == MATCHED_RECURSIVELY)
 				die(_("not removing '%s' recursively without -r"),
 				    *original ? original : ".");
 		}
 
+		if (only_match_skip_worktree.nr) {
+			advise_on_updating_sparse_paths(&only_match_skip_worktree);
+			ret = 1;
+		}
+		free(skip_worktree_seen);
+		string_list_clear(&only_match_skip_worktree, 0);
+
 		if (!seen_any)
-			exit(0);
+			exit(ret);
 	}
+	clear_pathspec(&pathspec);
+	free(seen);
 
 	if (!index_only)
 		submodules_absorb_gitdir_if_needed();
@@ -405,5 +422,5 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			       COMMIT_LOCK | SKIP_IF_UNCHANGED))
 		die(_("Unable to write new index file"));
 
-	return 0;
+	return ret;
 }
diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index d7da50ada5..a4bdd7c494 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -14,6 +14,7 @@
 #include "unpack-trees.h"
 #include "wt-status.h"
 #include "quote.h"
+#include "sparse-index.h"
 
 static const char *empty_base = "";
 
@@ -110,6 +111,8 @@ static int update_working_directory(struct pattern_list *pl)
 	if (is_index_unborn(r->index))
 		return UPDATE_SPARSITY_SUCCESS;
 
+	r->index->sparse_checkout_patterns = pl;
+
 	memset(&o, 0, sizeof(o));
 	o.verbose_update = isatty(2);
 	o.update = 1;
@@ -138,6 +141,7 @@ static int update_working_directory(struct pattern_list *pl)
 	else
 		rollback_lock_file(&lock_file);
 
+	r->index->sparse_checkout_patterns = NULL;
 	return result;
 }
 
@@ -276,16 +280,20 @@ static int set_config(enum sparse_checkout_mode mode)
 				      "core.sparseCheckoutCone",
 				      mode == MODE_CONE_PATTERNS ? "true" : NULL);
 
+	if (mode == MODE_NO_PATTERNS)
+		set_sparse_index_config(the_repository, 0);
+
 	return 0;
 }
 
 static char const * const builtin_sparse_checkout_init_usage[] = {
-	N_("git sparse-checkout init [--cone]"),
+	N_("git sparse-checkout init [--cone] [--[no-]sparse-index]"),
 	NULL
 };
 
 static struct sparse_checkout_init_opts {
 	int cone_mode;
+	int sparse_index;
 } init_opts;
 
 static int sparse_checkout_init(int argc, const char **argv)
@@ -300,11 +308,15 @@ static int sparse_checkout_init(int argc, const char **argv)
 	static struct option builtin_sparse_checkout_init_options[] = {
 		OPT_BOOL(0, "cone", &init_opts.cone_mode,
 			 N_("initialize the sparse-checkout in cone mode")),
+		OPT_BOOL(0, "sparse-index", &init_opts.sparse_index,
+			 N_("toggle the use of a sparse index")),
 		OPT_END(),
 	};
 
 	repo_read_index(the_repository);
 
+	init_opts.sparse_index = -1;
+
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_init_options,
 			     builtin_sparse_checkout_init_usage, 0);
@@ -323,10 +335,20 @@ 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);
-		core_apply_sparse_checkout = 1;
 		return update_working_directory(NULL);
 	}
 
@@ -348,6 +370,7 @@ static int sparse_checkout_init(int argc, const char **argv)
 	add_pattern(strbuf_detach(&pattern, NULL), empty_base, 0, &pl, 0);
 	strbuf_addstr(&pattern, "!/*/");
 	add_pattern(strbuf_detach(&pattern, NULL), empty_base, 0, &pl, 0);
+	pl.use_cone_patterns = init_opts.cone_mode;
 
 	return write_patterns_and_update(&pl);
 }
@@ -517,19 +540,18 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 {
 	int result;
 	int changed_config = 0;
-	struct pattern_list pl;
-	memset(&pl, 0, sizeof(pl));
+	struct pattern_list *pl = xcalloc(1, sizeof(*pl));
 
 	switch (m) {
 	case ADD:
 		if (core_sparse_checkout_cone)
-			add_patterns_cone_mode(argc, argv, &pl);
+			add_patterns_cone_mode(argc, argv, pl);
 		else
-			add_patterns_literal(argc, argv, &pl);
+			add_patterns_literal(argc, argv, pl);
 		break;
 
 	case REPLACE:
-		add_patterns_from_input(&pl, argc, argv);
+		add_patterns_from_input(pl, argc, argv);
 		break;
 	}
 
@@ -539,12 +561,13 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 		changed_config = 1;
 	}
 
-	result = write_patterns_and_update(&pl);
+	result = write_patterns_and_update(pl);
 
 	if (result && changed_config)
 		set_config(MODE_NO_PATTERNS);
 
-	clear_pattern_list(&pl);
+	clear_pattern_list(pl);
+	free(pl);
 	return result;
 }
 
@@ -614,6 +637,9 @@ static int sparse_checkout_disable(int argc, const char **argv)
 	strbuf_addstr(&match_all, "/*");
 	add_pattern(strbuf_detach(&match_all, NULL), empty_base, 0, &pl, 0);
 
+	prepare_repo_settings(the_repository);
+	the_repository->settings.sparse_index = 0;
+
 	if (update_working_directory(&pl))
 		die(_("error while refreshing working directory"));
 
diff --git a/builtin/stash.c b/builtin/stash.c
index c56fed3354..d68ed784d2 100644
--- a/builtin/stash.c
+++ b/builtin/stash.c
@@ -1412,6 +1412,8 @@ static int do_push_stash(const struct pathspec *ps, const char *stash_msg, int q
 		int i;
 		char *ps_matched = xcalloc(ps->nr, 1);
 
+		/* TODO: audit for interaction with sparse-index. */
+		ensure_full_index(&the_index);
 		for (i = 0; i < active_nr; i++)
 			ce_path_match(&the_index, active_cache[i], ps,
 				      ps_matched);
diff --git a/builtin/tag.c b/builtin/tag.c
index d403417b56..82fcfc0982 100644
--- a/builtin/tag.c
+++ b/builtin/tag.c
@@ -39,6 +39,8 @@ static int list_tags(struct ref_filter *filter, struct ref_sorting *sorting,
 		     struct ref_format *format)
 {
 	struct ref_array array;
+	struct strbuf output = STRBUF_INIT;
+	struct strbuf err = STRBUF_INIT;
 	char *to_free = NULL;
 	int i;
 
@@ -63,8 +65,17 @@ static int list_tags(struct ref_filter *filter, struct ref_sorting *sorting,
 	filter_refs(&array, filter, FILTER_REFS_TAGS);
 	ref_array_sort(sorting, &array);
 
-	for (i = 0; i < array.nr; i++)
-		show_ref_array_item(array.items[i], format);
+	for (i = 0; i < array.nr; i++) {
+		strbuf_reset(&output);
+		strbuf_reset(&err);
+		if (format_ref_array_item(array.items[i], format, &output, &err))
+			die("%s", err.buf);
+		fwrite(output.buf, 1, output.len, stdout);
+		putchar('\n');
+	}
+
+	strbuf_release(&err);
+	strbuf_release(&output);
 	ref_array_clear(&array);
 	free(to_free);
 
diff --git a/builtin/update-index.c b/builtin/update-index.c
index 79087bccea..f1f16f2de5 100644
--- a/builtin/update-index.c
+++ b/builtin/update-index.c
@@ -745,6 +745,8 @@ static int do_reupdate(int ac, const char **av,
 		 */
 		has_head = 0;
  redo:
+	/* TODO: audit for interaction with sparse-index. */
+	ensure_full_index(&the_index);
 	for (pos = 0; pos < active_nr; pos++) {
 		const struct cache_entry *ce = active_cache[pos];
 		struct cache_entry *old = NULL;