[RFC PATCH v4 00/19] Sparse checkout

@@ -24,8 +24,8 @@ static int info_only;
 static int force_remove;
 static int verbose;
 static int mark_valid_only;
-#define MARK_VALID 1
-#define UNMARK_VALID 2
+#define MARK_FLAG 1
+#define UNMARK_FLAG 2
 
 static void report(const char *fmt, ...)
 {

@@ -40,19 +40,15 @@ static void report(const char *fmt, ...)
 	va_end(vp);
 }
 
-static int mark_valid(const char *path)
+static int mark_ce_flags(const char *path, int flag, int mark)
 {
 	int namelen = strlen(path);
 	int pos = cache_name_pos(path, namelen);
 	if (0 <= pos) {
-		switch (mark_valid_only) {
-		case MARK_VALID:
-			active_cache[pos]->ce_flags |= CE_VALID;
-			break;
-		case UNMARK_VALID:
-			active_cache[pos]->ce_flags &= ~CE_VALID;
-			break;
-		}
+		if (mark)
+			active_cache[pos]->ce_flags |= flag;
+		else
+			active_cache[pos]->ce_flags &= ~flag;
 		cache_tree_invalidate_path(active_cache_tree, path);
 		active_cache_changed = 1;
 		return 0;

@@ -276,7 +272,7 @@ static void update_one(const char *path, const char *prefix, int prefix_length)
 		goto free_return;
 	}
 	if (mark_valid_only) {
-		if (mark_valid(p))
+		if (mark_ce_flags(p, CE_VALID, mark_valid_only == MARK_FLAG))
 			die("Unable to mark file %s", path);
 		goto free_return;
 	}

@@ -647,11 +643,11 @@ int cmd_update_index(int argc, const char **argv, const char *prefix)
 				continue;
 			}
 			if (!strcmp(path, "--assume-unchanged")) {
-				mark_valid_only = MARK_VALID;
+				mark_valid_only = MARK_FLAG;
 				continue;
 			}
 			if (!strcmp(path, "--no-assume-unchanged")) {
-				mark_valid_only = UNMARK_VALID;
+				mark_valid_only = UNMARK_FLAG;
 				continue;
 			}
 			if (!strcmp(path, "--info-only")) {

@@ -157,6 +157,7 @@ test-date
 test-delta
 test-dump-cache-tree
 test-genrandom
+test-index-version
 test-match-trees
 test-parse-options
 test-path-utils

@@ -1586,6 +1586,7 @@ TEST_PROGRAMS += test-parse-options$X
 TEST_PROGRAMS += test-path-utils$X
 TEST_PROGRAMS += test-sha1$X
 TEST_PROGRAMS += test-sigchain$X
+TEST_PROGRAMS += test-index-version$X
 
 all:: $(TEST_PROGRAMS)
 

@@ -0,0 +1,14 @@
+#include "cache.h"
+
+int main(int argc, const char **argv)
+{
+	struct cache_header hdr;
+	int version;
+
+	memset(&hdr,0,sizeof(hdr));
+	if (read(0, &hdr, sizeof(hdr)) != sizeof(hdr))
+		return 0;
+	version = ntohl(hdr.hdr_version);
+	printf("%d\n", version);
+	return 0;
+}

@@ -107,6 +107,7 @@ OPTIONS
 	Identify the file status with the following tags (followed by
 	a space) at the start of each line:
 	H::	cached
+	S::	skip-worktree
 	M::	unmerged
 	R::	removed/deleted
 	C::	modified/changed

@@ -15,6 +15,7 @@ SYNOPSIS
 	     [--cacheinfo <mode> <object> <file>]\*
 	     [--chmod=(+|-)x]
 	     [--assume-unchanged | --no-assume-unchanged]
+	     [--skip-worktree | --no-skip-worktree]
 	     [--ignore-submodules]
 	     [--really-refresh] [--unresolve] [--again | -g]
 	     [--info-only] [--index-info]

@@ -99,6 +100,13 @@ in the index e.g. when merging in a commit;
 thus, in case the assumed-untracked file is changed upstream,
 you will need to handle the situation manually.
 
+--skip-worktree::
+--no-skip-worktree::
+	When one of these flags is specified, the object name recorded
+	for the paths are not updated. Instead, these options
+	set and unset the "skip-worktree" bit for the paths. See
+	section "Skip-worktree bit" below for more information.
+
 -g::
 --again::
 	Runs 'git-update-index' itself on the paths whose index

@@ -304,6 +312,27 @@ M foo.c
 <9> now it checks with lstat(2) and finds it has been changed.
 
 
+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.
+
+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)
+
+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.
+
+
 Configuration
 -------------
 

@@ -37,6 +37,7 @@ static const char *tag_removed = "";
 static const char *tag_other = "";
 static const char *tag_killed = "";
 static const char *tag_modified = "";
+static const char *tag_skip_worktree = "";
 
 static void show_dir_entry(const char *tag, struct dir_entry *ent)
 {

@@ -178,7 +179,8 @@ static void show_files(struct dir_struct *dir, const char *prefix)
 				continue;
 			if (ce->ce_flags & CE_UPDATE)
 				continue;
-			show_ce_entry(ce_stage(ce) ? tag_unmerged : tag_cached, ce);
+			show_ce_entry(ce_stage(ce) ? tag_unmerged :
+				(ce_skip_worktree(ce) ? tag_skip_worktree : tag_cached), ce);
 		}
 	}
 	if (show_deleted | show_modified) {

@@ -490,6 +492,7 @@ int cmd_ls_files(int argc, const char **argv, const char *prefix)
 		tag_modified = "C ";
 		tag_other = "? ";
 		tag_killed = "K ";
+		tag_skip_worktree = "S ";
 	}
 	if (show_modified || show_others || show_deleted || (dir.flags & DIR_SHOW_IGNORED) || show_killed)
 		require_work_tree = 1;

@@ -24,6 +24,7 @@ static int info_only;
 static int force_remove;
 static int verbose;
 static int mark_valid_only;
+static int mark_skip_worktree_only;
 #define MARK_FLAG 1
 #define UNMARK_FLAG 2
 

@@ -276,6 +277,11 @@ static void update_one(const char *path, const char *prefix, int prefix_length)
 			die("Unable to mark file %s", path);
 		goto free_return;
 	}
+	if (mark_skip_worktree_only) {
+		if (mark_ce_flags(p, CE_SKIP_WORKTREE, mark_skip_worktree_only == MARK_FLAG))
+			die("Unable to mark file %s", path);
+		goto free_return;
+	}
 
 	if (force_remove) {
 		if (remove_file_from_cache(p))

@@ -384,7 +390,7 @@ static void read_index_info(int line_termination)
 }
 
 static const char update_index_usage[] =
-"git update-index [-q] [--add] [--replace] [--remove] [--unmerged] [--refresh] [--really-refresh] [--cacheinfo] [--chmod=(+|-)x] [--assume-unchanged] [--info-only] [--force-remove] [--stdin] [--index-info] [--unresolve] [--again | -g] [--ignore-missing] [-z] [--verbose] [--] <file>...";
+"git update-index [-q] [--add] [--replace] [--remove] [--unmerged] [--refresh] [--really-refresh] [--cacheinfo] [--chmod=(+|-)x] [--assume-unchanged] [--skip-worktree|--no-skip-worktree] [--info-only] [--force-remove] [--stdin] [--index-info] [--unresolve] [--again | -g] [--ignore-missing] [-z] [--verbose] [--] <file>...";
 
 static unsigned char head_sha1[20];
 static unsigned char merge_head_sha1[20];

@@ -650,6 +656,14 @@ int cmd_update_index(int argc, const char **argv, const char *prefix)
 				mark_valid_only = UNMARK_FLAG;
 				continue;
 			}
+			if (!strcmp(path, "--no-skip-worktree")) {
+				mark_skip_worktree_only = UNMARK_FLAG;
+				continue;
+			}
+			if (!strcmp(path, "--skip-worktree")) {
+				mark_skip_worktree_only = MARK_FLAG;
+				continue;
+			}
 			if (!strcmp(path, "--info-only")) {
 				info_only = 1;
 				continue;

@@ -181,10 +181,11 @@ struct cache_entry {
  * Extended on-disk flags
  */
 #define CE_INTENT_TO_ADD 0x20000000
+#define CE_SKIP_WORKTREE 0x40000000
 /* CE_EXTENDED2 is for future extension */
 #define CE_EXTENDED2 0x80000000
 
-#define CE_EXTENDED_FLAGS (CE_INTENT_TO_ADD)
+#define CE_EXTENDED_FLAGS (CE_INTENT_TO_ADD | CE_SKIP_WORKTREE)
 
 /*
  * Safeguard to avoid saving wrong flags:

@@ -233,6 +234,7 @@ static inline size_t ce_namelen(const struct cache_entry *ce)
 			    ondisk_cache_entry_size(ce_namelen(ce)))
 #define ce_stage(ce) ((CE_STAGEMASK & (ce)->ce_flags) >> CE_STAGESHIFT)
 #define ce_uptodate(ce) ((ce)->ce_flags & CE_UPTODATE)
+#define ce_skip_worktree(ce) ((ce)->ce_flags & CE_SKIP_WORKTREE)
 #define ce_mark_uptodate(ce) ((ce)->ce_flags |= CE_UPTODATE)
 
 #define ce_permissions(mode) (((mode) & 0100) ? 0755 : 0644)

@@ -0,0 +1,57 @@
+#!/bin/sh
+#
+# Copyright (c) 2008 Nguyễn Thái Ngọc Duy
+#
+
+test_description='skip-worktree bit test'
+
+. ./test-lib.sh
+
+cat >expect.full <<EOF
+H 1
+H 2
+H sub/1
+H sub/2
+EOF
+
+cat >expect.skip <<EOF
+S 1
+H 2
+S sub/1
+H sub/2
+EOF
+
+test_expect_success 'setup' '
+	mkdir sub &&
+	touch ./1 ./2 sub/1 sub/2 &&
+	git add 1 2 sub/1 sub/2 &&
+	git ls-files -t | test_cmp expect.full -
+'
+
+test_expect_success 'index is at version 2' '
+	test "$(test-index-version < .git/index)" = 2
+'
+
+test_expect_success 'update-index --skip-worktree' '
+	git update-index --skip-worktree 1 sub/1 &&
+	git ls-files -t | test_cmp expect.skip -
+'
+
+test_expect_success 'index is at version 3 after having some skip-worktree entries' '
+	test "$(test-index-version < .git/index)" = 3
+'
+
+test_expect_success 'ls-files -t' '
+	git ls-files -t | test_cmp expect.skip -
+'
+
+test_expect_success 'update-index --no-skip-worktree' '
+	git update-index --no-skip-worktree 1 sub/1 &&
+	git ls-files -t | test_cmp expect.full -
+'
+
+test_expect_success 'index version is back to 2 when there is no skip-worktree entry' '
+	test "$(test-index-version < .git/index)" = 2
+'
+
+test_done

@@ -181,6 +181,11 @@ static void add_remove_files(struct string_list *list)
 	for (i = 0; i < list->nr; i++) {
 		struct stat st;
 		struct string_list_item *p = &(list->items[i]);
+		int pos = index_name_pos(&the_index, p->string, strlen(p->string));
+		struct cache_entry *ce = pos < 0 ? NULL : active_cache[pos];
+
+		if (ce && ce_skip_worktree(ce))
+			continue;
 
 		if (!lstat(p->string, &st)) {
 			if (add_to_cache(p->string, &st, 0))

@@ -517,7 +517,7 @@ static int grep_cache(struct grep_opt *opt, const char **paths, int cached,
 		 * are identical, even if worktree file has been modified, so use
 		 * cache version instead
 		 */
-		if (cached || (ce->ce_flags & CE_VALID)) {
+		if (cached || (ce->ce_flags & CE_VALID) || ce_skip_worktree(ce)) {
 			if (ce_stage(ce))
 				continue;
 			hit |= grep_sha1(opt, ce->sha1, ce->name, 0);

@@ -194,6 +194,8 @@ static void show_files(struct dir_struct *dir, const char *prefix)
 				continue;
 			if (ce->ce_flags & CE_UPDATE)
 				continue;
+			if (ce_skip_worktree(ce))
+				continue;
 			err = lstat(ce->name, &st);
 			if (show_deleted && err)
 				show_ce_entry(tag_removed, ce);

@@ -172,29 +172,29 @@ static int process_directory(const char *path, int len, struct stat *st)
 	return error("%s: is a directory - add files inside instead", path);
 }
 
-/*
- * Process a regular file
- */
-static int process_file(const char *path, int len, struct stat *st)
-{
-	int pos = cache_name_pos(path, len);
-	struct cache_entry *ce = pos < 0 ? NULL : active_cache[pos];
-
-	if (ce && S_ISGITLINK(ce->ce_mode))
-		return error("%s is already a gitlink, not replacing", path);
-
-	return add_one_path(ce, path, len, st);
-}
-
 static int process_path(const char *path)
 {
-	int len;
+	int pos, len;
 	struct stat st;
+	struct cache_entry *ce;
 
 	len = strlen(path);
 	if (has_symlink_leading_path(path, len))
 		return error("'%s' is beyond a symbolic link", path);
 
+	pos = cache_name_pos(path, len);
+	ce = pos < 0 ? NULL : active_cache[pos];
+	if (ce && ce_skip_worktree(ce)) {
+		/*
+		 * working directory version is assumed "good"
+		 * so updating it does not make sense.
+		 * On the other hand, removing it from index should work
+		 */
+		if (allow_remove && remove_file_from_cache(path))
+			return error("%s: cannot remove from the index", path);
+		return 0;
+	}
+
 	/*
 	 * First things first: get the stat information, to decide
 	 * what to do about the pathname!

@@ -205,7 +205,13 @@ static int process_path(const char *path)
 	if (S_ISDIR(st.st_mode))
 		return process_directory(path, len, &st);
 
-	return process_file(path, len, &st);
+	/*
+	 * Process a regular file
+	 */
+	if (ce && S_ISGITLINK(ce->ce_mode))
+		return error("%s is already a gitlink, not replacing", path);
+
+	return add_one_path(ce, path, len, &st);
 }
 
 static int add_cacheinfo(unsigned int mode, const unsigned char *sha1,

@@ -159,7 +159,7 @@ int run_diff_files(struct rev_info *revs, unsigned int option)
 				continue;
 		}
 
-		if (ce_uptodate(ce))
+		if (ce_uptodate(ce) || ce_skip_worktree(ce))
 			continue;
 
 		changed = check_removed(ce, &st);

@@ -321,6 +321,8 @@ static void do_oneway_diff(struct unpack_trees_options *o,
 	struct rev_info *revs = o->unpack_data;
 	int match_missing, cached;
 
+	/* if the entry is not checked out, don't examine work tree */
+	cached = o->index_only || (idx && ce_skip_worktree(idx));
 	/*
 	 * Backward compatibility wart - "diff-index -m" does
 	 * not mean "do not ignore merges", but "match_missing".

@@ -328,7 +330,6 @@ static void do_oneway_diff(struct unpack_trees_options *o,
 	 * But with the revision flag parsing, that's found in
 	 * "!revs->ignore_merges".
 	 */
-	cached = o->index_only;
 	match_missing = !revs->ignore_merges;
 
 	if (cached && idx && ce_stage(idx)) {

@@ -1805,7 +1805,7 @@ static int reuse_worktree_file(const char *name, const unsigned char *sha1, int
 	 * If ce is marked as "assume unchanged", there is no
 	 * guarantee that work tree matches what we are looking for.
 	 */
-	if (ce->ce_flags & CE_VALID)
+	if ((ce->ce_flags & CE_VALID) || ce_skip_worktree(ce))
 		return 0;
 
 	/*

@@ -265,7 +265,7 @@ int ie_match_stat(const struct index_state *istate,
 	 * If it's marked as always valid in the index, it's
 	 * valid whatever the checked-out copy says.
 	 */
-	if (!ignore_valid && (ce->ce_flags & CE_VALID))
+	if (!ignore_valid && ((ce->ce_flags & CE_VALID) || ce_skip_worktree(ce)))
 		return 0;
 
 	/*

@@ -1004,11 +1004,7 @@ static struct cache_entry *refresh_cache_ent(struct index_state *istate,
 	if (ce_uptodate(ce))
 		return ce;
 
-	/*
-	 * CE_VALID means the user promised us that the change to
-	 * the work tree does not matter and told us not to worry.
-	 */
-	if (!ignore_valid && (ce->ce_flags & CE_VALID)) {
+	if (!ignore_valid && ((ce->ce_flags & CE_VALID) || ce_skip_worktree(ce))) {
 		ce_mark_uptodate(ce);
 		return ce;
 	}

@@ -0,0 +1,163 @@
+#!/bin/sh
+#
+# Copyright (c) 2008 Nguyễn Thái Ngọc Duy
+#
+
+test_description='skip-worktree bit test'
+
+. ./test-lib.sh
+
+cat >expect.full <<EOF
+H 1
+H 2
+H init.t
+H sub/1
+H sub/2
+EOF
+
+cat >expect.skip <<EOF
+S 1
+H 2
+H init.t
+S sub/1
+H sub/2
+EOF
+
+NULL_SHA1=e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
+ZERO_SHA0=0000000000000000000000000000000000000000
+setup_absent() {
+	test -f 1 && rm 1
+	git update-index --remove 1 &&
+	git update-index --add --cacheinfo 100644 $NULL_SHA1 1 &&
+	git update-index --skip-worktree 1
+}
+
+test_absent() {
+	echo "100644 $NULL_SHA1 0	1" > expected &&
+	git ls-files --stage 1 > result &&
+	test_cmp expected result &&
+	test ! -f 1
+}
+
+setup_dirty() {
+	git update-index --force-remove 1 &&
+	echo dirty > 1 &&
+	git update-index --add --cacheinfo 100644 $NULL_SHA1 1 &&
+	git update-index --skip-worktree 1
+}
+
+test_dirty() {
+	echo "100644 $NULL_SHA1 0	1" > expected &&
+	git ls-files --stage 1 > result &&
+	test_cmp expected result &&
+	echo dirty > expected
+	test_cmp expected 1
+}
+
+test_expect_success 'setup' '
+	test_commit init &&
+	mkdir sub &&
+	touch ./1 ./2 sub/1 sub/2 &&
+	git add 1 2 sub/1 sub/2 &&
+	git update-index --skip-worktree 1 sub/1 &&
+	git ls-files -t > result &&
+	test_cmp expect.skip result
+'
+
+test_expect_success 'update-index' '
+	setup_absent &&
+	git update-index 1 &&
+	test_absent
+'
+
+test_expect_success 'update-index' '
+	setup_dirty &&
+	git update-index 1 &&
+	test_dirty
+'
+
+test_expect_success 'update-index --remove' '
+	setup_absent &&
+	git update-index --remove 1 &&
+	test -z "$(git ls-files 1)" &&
+	test ! -f 1
+'
+
+test_expect_success 'update-index --remove' '
+	setup_dirty &&
+	git update-index --remove 1 &&
+	test -z "$(git ls-files 1)" &&
+	echo dirty > expected &&
+	test_cmp expected 1
+'
+
+test_expect_success 'ls-files --delete' '
+	setup_absent &&
+	test -z "$(git ls-files -d)"
+'
+
+test_expect_success 'ls-files --delete' '
+	setup_dirty &&
+	test -z "$(git ls-files -d)"
+'
+
+test_expect_success 'ls-files --modified' '
+	setup_absent &&
+	test -z "$(git ls-files -m)"
+'
+
+test_expect_success 'ls-files --modified' '
+	setup_dirty &&
+	test -z "$(git ls-files -m)"
+'
+
+test_expect_success 'grep with skip-worktree file' '
+	git update-index --no-skip-worktree 1 &&
+	echo test > 1 &&
+	git update-index 1 &&
+	git update-index --skip-worktree 1 &&
+	rm 1 &&
+	test "$(git grep --no-ext-grep test)" = "1:test"
+'
+
+echo ":000000 100644 $ZERO_SHA0 $NULL_SHA1 A	1" > expected
+test_expect_success 'diff-index does not examine skip-worktree absent entries' '
+	setup_absent &&
+	git diff-index HEAD -- 1 > result &&
+	test_cmp expected result
+'
+
+test_expect_success 'diff-index does not examine skip-worktree dirty entries' '
+	setup_dirty &&
+	git diff-index HEAD -- 1 > result &&
+	test_cmp expected result
+'
+
+test_expect_success 'diff-files does not examine skip-worktree absent entries' '
+	setup_absent &&
+	test -z "$(git diff-files -- one)"
+'
+
+test_expect_success 'diff-files does not examine skip-worktree dirty entries' '
+	setup_dirty &&
+	test -z "$(git diff-files -- one)"
+'
+
+test_expect_success 'git-rm succeeds on skip-worktree absent entries' '
+	setup_absent &&
+	git rm 1
+'
+
+test_expect_failure 'commit on skip-worktree absent entries' '
+	git reset &&
+	setup_absent &&
+	test_must_fail git commit -m null 1
+'
+
+test_expect_failure 'commit on skip-worktree dirty entries' '
+	git reset &&
+	setup_dirty &&
+	test_must_fail git commit -m null 1
+'
+
+test_done

@@ -0,0 +1,146 @@
+#!/bin/sh
+#
+# Copyright (c) 2008 Nguyễn Thái Ngọc Duy
+#
+
+test_description='test worktree writing operations when skip-worktree is used'
+
+. ./test-lib.sh
+
+test_expect_success 'setup' '
+	test_commit init &&
+	echo modified >> init.t &&
+	touch added &&
+	git add init.t added &&
+	git commit -m "modified and added" &&
+	git tag top
+'
+
+test_expect_success 'read-tree updates worktree, absent case' '
+	git checkout -f top &&
+	git update-index --skip-worktree init.t &&
+	rm init.t &&
+	git read-tree -m -u HEAD^ &&
+	echo init > expected &&
+	test_cmp expected init.t
+'
+
+test_expect_success 'read-tree updates worktree, dirty case' '
+	git checkout -f top &&
+	git update-index --skip-worktree init.t &&
+	echo dirty >> init.t &&
+	test_must_fail git read-tree -m -u HEAD^ &&
+	grep -q dirty init.t &&
+	test "$(git ls-files -t init.t)" = "S init.t" &&
+	git update-index --no-skip-worktree init.t
+'
+
+test_expect_success 'read-tree removes worktree, absent case' '
+	git checkout -f top &&
+	git update-index --skip-worktree added &&
+	rm added &&
+	git read-tree -m -u HEAD^ &&
+	test ! -f added
+'
+
+test_expect_success 'read-tree removes worktree, dirty case' '
+	git checkout -f top &&
+	git update-index --skip-worktree added &&
+	echo dirty >> added &&
+	test_must_fail git read-tree -m -u HEAD^ &&
+	grep -q dirty added &&
+	test "$(git ls-files -t added)" = "S added" &&
+	git update-index --no-skip-worktree added
+'
+
+NULL_SHA1=e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
+ZERO_SHA0=0000000000000000000000000000000000000000
+setup_absent() {
+	test -f 1 && rm 1
+	git update-index --remove 1 &&
+	git update-index --add --cacheinfo 100644 $NULL_SHA1 1 &&
+	git update-index --skip-worktree 1
+}
+
+test_absent() {
+	echo "100644 $NULL_SHA1 0	1" > expected &&
+	git ls-files --stage 1 > result &&
+	test_cmp expected result &&
+	test ! -f 1
+}
+
+setup_dirty() {
+	git update-index --force-remove 1 &&
+	echo dirty > 1 &&
+	git update-index --add --cacheinfo 100644 $NULL_SHA1 1 &&
+	git update-index --skip-worktree 1
+}
+
+test_dirty() {
+	echo "100644 $NULL_SHA1 0	1" > expected &&
+	git ls-files --stage 1 > result &&
+	test_cmp expected result &&
+	echo dirty > expected
+	test_cmp expected 1
+}
+
+cat >expected <<EOF
+S 1
+H 2
+H init.t
+S sub/1
+H sub/2
+EOF
+
+test_expect_success 'index setup' '
+	git checkout -f init &&
+	mkdir sub &&
+	touch ./1 ./2 sub/1 sub/2 &&
+	git add 1 2 sub/1 sub/2 &&
+	git update-index --skip-worktree 1 sub/1 &&
+	git ls-files -t > result &&
+	test_cmp expected result
+'
+
+test_expect_success 'git-add ignores worktree content' '
+	setup_absent &&
+	git add 1 &&
+	test_absent
+'
+
+test_expect_success 'git-add ignores worktree content' '
+	setup_dirty &&
+	git add 1 &&
+	test_dirty
+'
+
+test_expect_success 'git-rm fails if worktree is dirty' '
+	setup_dirty &&
+	test_must_fail git rm 1 &&
+	test_dirty
+'
+
+cat >expected <<EOF
+Would remove expected
+Would remove result
+EOF
+test_expect_success 'git-clean, absent case' '
+	setup_absent &&
+	git clean -n > result &&
+	test_cmp expected result
+'
+
+test_expect_success 'git-clean, dirty case' '
+	setup_dirty &&
+	git clean -n > result &&
+	test_cmp expected result
+'
+
+test_expect_failure 'git-apply adds file' false
+test_expect_failure 'git-apply updates file' false
+test_expect_failure 'git-apply removes file' false
+test_expect_failure 'git-mv to skip-worktree' false
+test_expect_failure 'git-mv from skip-worktree' false
+test_expect_failure 'git-checkout' false
+
+test_done

@@ -450,7 +450,7 @@ static int verify_uptodate(struct cache_entry *ce,
 {
 	struct stat st;
 
-	if (o->index_only || o->reset || ce_uptodate(ce))
+	if (o->index_only || (!ce_skip_worktree(ce) && (o->reset || ce_uptodate(ce))))
 		return 0;
 
 	if (!lstat(ce->name, &st)) {

@@ -1004,7 +1004,7 @@ int oneway_merge(struct cache_entry **src, struct unpack_trees_options *o)
 
 	if (old && same(old, a)) {
 		int update = 0;
-		if (o->reset && !ce_uptodate(old)) {
+		if (o->reset && !ce_uptodate(old) && !ce_skip_worktree(old)) {
 			struct stat st;
 			if (lstat(old->name, &st) ||
 			    ie_match_stat(o->src_index, old, &st, CE_MATCH_IGNORE_VALID))

@@ -229,10 +229,9 @@ static int add_excludes_from_file_1(const char *fname,
 
 	if (buf_p)
 		*buf_p = buf;
-	buf[size++] = '\n';
 	entry = buf;
-	for (i = 0; i < size; i++) {
-		if (buf[i] == '\n') {
+	for (i = 0; i <= size; i++) {
+		if (i == size || buf[i] == '\n') {
 			if (entry != buf + i && entry[0] != '#') {
 				buf[i - (i && buf[i-1] == '\r')] = 0;
 				add_exclude(entry, base, baselen, which);

@@ -58,6 +58,9 @@ The result of the enumeration is left in these fields::
 Calling sequence
 ----------------
 
+Note: index may be looked at for .gitignore files that are CE_SKIP_WORKTREE
+marked. If you to exclude files, make sure you have loaded index first.
+
 * Prepare `struct dir_struct dir` and clear it with `memset(&dir, 0,
   sizeof(dir))`.
 

@@ -75,11 +75,13 @@ int cmd_clean(int argc, const char **argv, const char *prefix)
 
 	dir.flags |= DIR_SHOW_OTHER_DIRECTORIES;
 
+	if (read_cache() < 0)
+		die("index file corrupt");
+
 	if (!ignored)
 		setup_standard_excludes(&dir);
 
 	pathspec = get_pathspec(prefix, argv);
-	read_cache();
 
 	fill_directory(&dir, pathspec);
 

@@ -485,6 +485,9 @@ int cmd_ls_files(int argc, const char **argv, const char *prefix)
 		prefix_offset = strlen(prefix);
 	git_config(git_default_config, NULL);
 
+	if (read_cache() < 0)
+		die("index file corrupt");
+
 	argc = parse_options(argc, argv, prefix, builtin_ls_files_options,
 			ls_files_usage, 0);
 	if (show_tag || show_valid_bit) {

@@ -513,7 +516,6 @@ int cmd_ls_files(int argc, const char **argv, const char *prefix)
 	pathspec = get_pathspec(prefix, argv);
 
 	/* be nice with submodule paths ending in a slash */
-	read_cache();
 	if (pathspec)
 		strip_trailing_slash_from_submodules();
 

@@ -200,11 +200,35 @@ void add_exclude(const char *string, const char *base,
 	which->excludes[which->nr++] = x;
 }
 
+static void *read_skip_worktree_file_from_index(const char *path, size_t *size)
+{
+	int pos, len;
+	unsigned long sz;
+	enum object_type type;
+	void *data;
+	struct index_state *istate = &the_index;
+
+	len = strlen(path);
+	pos = index_name_pos(istate, path, len);
+	if (pos < 0)
+		return NULL;
+	if (!ce_skip_worktree(istate->cache[pos]))
+		return NULL;
+	data = read_sha1_file(istate->cache[pos]->sha1, &type, &sz);
+	if (!data || type != OBJ_BLOB) {
+		free(data);
+		return NULL;
+	}
+	*size = xsize_t(sz);
+	return data;
+}
+
 static int add_excludes_from_file_1(const char *fname,
 				    const char *base,
 				    int baselen,
 				    char **buf_p,
-				    struct exclude_list *which)
+				    struct exclude_list *which,
+				    int check_index)
 {
 	struct stat st;
 	int fd, i;

@@ -212,20 +236,26 @@ static int add_excludes_from_file_1(const char *fname,
 	char *buf, *entry;
 
 	fd = open(fname, O_RDONLY);
-	if (fd < 0 || fstat(fd, &st) < 0)
-		goto err;
-	size = xsize_t(st.st_size);
-	if (size == 0) {
-		close(fd);
-		return 0;
+	if (fd < 0 || fstat(fd, &st) < 0) {
+		if (0 <= fd)
+			close(fd);
+		if (!check_index ||
+		    (buf = read_skip_worktree_file_from_index(fname, &size)) == NULL)
+			return -1;
 	}
-	buf = xmalloc(size+1);
-	if (read_in_full(fd, buf, size) != size)
-	{
-		free(buf);
-		goto err;
+	else {
+		size = xsize_t(st.st_size);
+		if (size == 0) {
+			close(fd);
+			return 0;
+		}
+		buf = xmalloc(size);
+		if (read_in_full(fd, buf, size) != size) {
+			close(fd);
+			return -1;
+		}
+		close(fd);
 	}
-	close(fd);
 
 	if (buf_p)
 		*buf_p = buf;

@@ -240,17 +270,12 @@ static int add_excludes_from_file_1(const char *fname,
 		}
 	}
 	return 0;
-
- err:
-	if (0 <= fd)
-		close(fd);
-	return -1;
 }
 
 void add_excludes_from_file(struct dir_struct *dir, const char *fname)
 {
 	if (add_excludes_from_file_1(fname, "", 0, NULL,
-				     &dir->exclude_list[EXC_FILE]) < 0)
+				     &dir->exclude_list[EXC_FILE], 0) < 0)
 		die("cannot use %s as an exclude file", fname);
 }
 

@@ -301,7 +326,7 @@ static void prep_exclude(struct dir_struct *dir, const char *base, int baselen)
 		strcpy(dir->basebuf + stk->baselen, dir->exclude_per_dir);
 		add_excludes_from_file_1(dir->basebuf,
 					 dir->basebuf, stk->baselen,
-					 &stk->filebuf, el);
+					 &stk->filebuf, el, 1);
 		dir->exclude_stack = stk;
 		current = stk->baselen;
 	}

@@ -64,6 +64,8 @@ two/*.4
 echo '!*.2
 !*.8' >one/two/.gitignore
 
+allignores='.gitignore one/.gitignore one/two/.gitignore'
+
 test_expect_success \
     'git ls-files --others with various exclude options.' \
     'git ls-files --others \

@@ -85,6 +87,26 @@ test_expect_success \
        >output &&
      test_cmp expect output'
 
+test_expect_success 'setup skip-worktree gitignore' '
+	git add $allignores &&
+	git update-index --skip-worktree $allignores &&
+	rm $allignores
+'
+
+test_expect_success \
+    'git ls-files --others with various exclude options.' \
+    'git ls-files --others \
+       --exclude=\*.6 \
+       --exclude-per-directory=.gitignore \
+       --exclude-from=.git/ignore \
+       >output &&
+     test_cmp expect output'
+
+test_expect_success 'restore gitignore' '
+	git checkout $allignores &&
+	rm .git/index
+'
+
 cat > excludes-file <<\EOF
 *.[1-8]
 e*

@@ -22,6 +22,25 @@ test_expect_success 'setup' '
 
 '
 
+test_expect_success 'git clean with skip-worktree .gitignore' '
+	git update-index --skip-worktree .gitignore &&
+	rm .gitignore &&
+	mkdir -p build docs &&
+	touch a.out src/part3.c docs/manual.txt obj.o build/lib.so &&
+	git clean &&
+	test -f Makefile &&
+	test -f README &&
+	test -f src/part1.c &&
+	test -f src/part2.c &&
+	test ! -f a.out &&
+	test ! -f src/part3.c &&
+	test -f docs/manual.txt &&
+	test -f obj.o &&
+	test -f build/lib.so &&
+	git update-index --no-skip-worktree .gitignore &&
+	git checkout .gitignore
+'
+
 test_expect_success 'git clean' '
 
 	mkdir -p build docs &&

@@ -680,6 +680,8 @@ static int merged_entry(struct cache_entry *merge, struct cache_entry *old,
 		} else {
 			if (verify_uptodate(old, o))
 				return -1;
+			if (ce_skip_worktree(old))
+				update |= CE_SKIP_WORKTREE;
 			invalidate_ce_path(old, o);
 		}
 	}

@@ -223,12 +223,12 @@ static void *read_skip_worktree_file_from_index(const char *path, size_t *size)
 	return data;
 }
 
-static int add_excludes_from_file_1(const char *fname,
-				    const char *base,
-				    int baselen,
-				    char **buf_p,
-				    struct exclude_list *which,
-				    int check_index)
+int add_excludes_from_file_to_list(const char *fname,
+				   const char *base,
+				   int baselen,
+				   char **buf_p,
+				   struct exclude_list *which,
+				   int check_index)
 {
 	struct stat st;
 	int fd, i;

@@ -274,8 +274,8 @@ static int add_excludes_from_file_1(const char *fname,
 
 void add_excludes_from_file(struct dir_struct *dir, const char *fname)
 {
-	if (add_excludes_from_file_1(fname, "", 0, NULL,
-				     &dir->exclude_list[EXC_FILE], 0) < 0)
+	if (add_excludes_from_file_to_list(fname, "", 0, NULL,
+					   &dir->exclude_list[EXC_FILE], 0) < 0)
 		die("cannot use %s as an exclude file", fname);
 }
 

@@ -324,9 +324,9 @@ static void prep_exclude(struct dir_struct *dir, const char *base, int baselen)
 		memcpy(dir->basebuf + current, base + current,
 		       stk->baselen - current);
 		strcpy(dir->basebuf + stk->baselen, dir->exclude_per_dir);
-		add_excludes_from_file_1(dir->basebuf,
-					 dir->basebuf, stk->baselen,
-					 &stk->filebuf, el, 1);
+		add_excludes_from_file_to_list(dir->basebuf,
+					       dir->basebuf, stk->baselen,
+					       &stk->filebuf, el, 1);
 		dir->exclude_stack = stk;
 		current = stk->baselen;
 	}

@@ -336,9 +336,9 @@ static void prep_exclude(struct dir_struct *dir, const char *base, int baselen)
 /* Scan the list and let the last match determine the fate.
  * Return 1 for exclude, 0 for include and -1 for undecided.
  */
-static int excluded_1(const char *pathname,
-		      int pathlen, const char *basename, int *dtype,
-		      struct exclude_list *el)
+int excluded_from_list(const char *pathname,
+		       int pathlen, const char *basename, int *dtype,
+		       struct exclude_list *el)
 {
 	int i;
 

@@ -412,8 +412,8 @@ int excluded(struct dir_struct *dir, const char *pathname, int *dtype_p)
 
 	prep_exclude(dir, pathname, basename-pathname);
 	for (st = EXC_CMDL; st <= EXC_FILE; st++) {
-		switch (excluded_1(pathname, pathlen, basename,
-				   dtype_p, &dir->exclude_list[st])) {
+		switch (excluded_from_list(pathname, pathlen, basename,
+					   dtype_p, &dir->exclude_list[st])) {
 		case 0:
 			return 0;
 		case 1:

@@ -69,7 +69,11 @@ extern int match_pathspec(const char **pathspec, const char *name, int namelen,
 extern int fill_directory(struct dir_struct *dir, const char **pathspec);
 extern int read_directory(struct dir_struct *, const char *path, int len, const char **pathspec);
 
+extern int excluded_from_list(const char *pathname, int pathlen, const char *basename,
+			      int *dtype, struct exclude_list *el);
 extern int excluded(struct dir_struct *, const char *, int *);
+extern int add_excludes_from_file_to_list(const char *fname, const char *base, int baselen,
+					  char **buf_p, struct exclude_list *which, int check_index);
 extern void add_excludes_from_file(struct dir_struct *, const char *fname);
 extern void add_exclude(const char *string, const char *base,
 			int baselen, struct exclude_list *which);