1 files changed, 222 insertions, 162 deletions

diff --git a/builtin/apply.c b/builtin/apply.c
index 156b3ce3b7..0aad912839 100644
--- a/builtin/apply.c
+++ b/builtin/apply.c
@@ -7,6 +7,7 @@
  *
  */
 #include "cache.h"
+#include "lockfile.h"
 #include "cache-tree.h"
 #include "quote.h"
 #include "blob.h"
@@ -300,11 +301,13 @@ static int fuzzy_matchlines(const char *s1, size_t n1,
 	while ((*last2 == '\r') || (*last2 == '\n'))
 		last2--;
 
-	/* skip leading whitespace */
-	while (isspace(*s1) && (s1 <= last1))
-		s1++;
-	while (isspace(*s2) && (s2 <= last2))
-		s2++;
+	/* skip leading whitespaces, if both begin with whitespace */
+	if (s1 <= last1 && s2 <= last2 && isspace(*s1) && isspace(*s2)) {
+		while (isspace(*s1) && (s1 <= last1))
+			s1++;
+		while (isspace(*s2) && (s2 <= last2))
+			s2++;
+	}
 	/* early return if both lines are empty */
 	if ((s1 > last1) && (s2 > last2))
 		return 1;
@@ -433,7 +436,7 @@ static unsigned long linelen(const char *buffer, unsigned long size)
 
 static int is_dev_null(const char *str)
 {
-	return !memcmp("/dev/null", str, 9) && isspace(str[9]);
+	return skip_prefix(str, "/dev/null", &str) && isspace(*str);
 }
 
 #define TERM_SPACE	1
@@ -473,7 +476,7 @@ static char *find_name_gnu(const char *line, const char *def, int p_value)
 
 	/*
 	 * Proposed "new-style" GNU patch/diff format; see
-	 * http://marc.theaimsgroup.com/?l=git&m=112927316408690&w=2
+	 * http://marc.info/?l=git&m=112927316408690&w=2
 	 */
 	if (unquote_c_style(&name, line, NULL)) {
 		strbuf_release(&name);
@@ -722,7 +725,7 @@ static char *find_name(const char *line, char *def, int p_value, int terminate)
 
 static char *find_name_traditional(const char *line, char *def, int p_value)
 {
-	size_t len = strlen(line);
+	size_t len;
 	size_t date_len;
 
 	if (*line == '"') {
@@ -906,7 +909,7 @@ static void parse_traditional_patch(const char *first, const char *second, struc
 			patch->old_name = name;
 		} else {
 			patch->old_name = name;
-			patch->new_name = xstrdup(name);
+			patch->new_name = null_strdup(name);
 		}
 	}
 	if (!name)
@@ -1041,15 +1044,17 @@ static int gitdiff_renamedst(const char *line, struct patch *patch)
 
 static int gitdiff_similarity(const char *line, struct patch *patch)
 {
-	if ((patch->score = strtoul(line, NULL, 10)) == ULONG_MAX)
-		patch->score = 0;
+	unsigned long val = strtoul(line, NULL, 10);
+	if (val <= 100)
+		patch->score = val;
 	return 0;
 }
 
 static int gitdiff_dissimilarity(const char *line, struct patch *patch)
 {
-	if ((patch->score = strtoul(line, NULL, 10)) == ULONG_MAX)
-		patch->score = 0;
+	unsigned long val = strtoul(line, NULL, 10);
+	if (val <= 100)
+		patch->score = val;
 	return 0;
 }
 
@@ -1071,7 +1076,7 @@ static int gitdiff_index(const char *line, struct patch *patch)
 
 	line = ptr + 2;
 	ptr = strchr(line, ' ');
-	eol = strchr(line, '\n');
+	eol = strchrnul(line, '\n');
 
 	if (!ptr || eol < ptr)
 		ptr = eol;
@@ -1277,9 +1282,7 @@ static int parse_git_header(const char *line, int len, unsigned int size, struct
 	 */
 	patch->def_name = git_header_name(line, len);
 	if (patch->def_name && root) {
-		char *s = xmalloc(root_len + strlen(patch->def_name) + 1);
-		strcpy(s, root);
-		strcpy(s + root_len, patch->def_name);
+		char *s = xstrfmt("%s%s", root, patch->def_name);
 		free(patch->def_name);
 		patch->def_name = s;
 	}
@@ -1407,10 +1410,10 @@ static void recount_diff(const char *line, int size, struct fragment *fragment)
 		case '\\':
 			continue;
 		case '@':
-			ret = size < 3 || prefixcmp(line, "@@ ");
+			ret = size < 3 || !starts_with(line, "@@ ");
 			break;
 		case 'd':
-			ret = size < 5 || prefixcmp(line, "diff ");
+			ret = size < 5 || !starts_with(line, "diff ");
 			break;
 		default:
 			ret = -1;
@@ -1796,11 +1799,11 @@ static struct fragment *parse_binary_hunk(char **buf_p,
 
 	*status_p = 0;
 
-	if (!prefixcmp(buffer, "delta ")) {
+	if (starts_with(buffer, "delta ")) {
 		patch_method = BINARY_DELTA_DEFLATED;
 		origlen = strtoul(buffer + 6, NULL, 10);
 	}
-	else if (!prefixcmp(buffer, "literal ")) {
+	else if (starts_with(buffer, "literal ")) {
 		patch_method = BINARY_LITERAL_DEFLATED;
 		origlen = strtoul(buffer + 8, NULL, 10);
 	}
@@ -1918,8 +1921,68 @@ static int parse_binary(char *buffer, unsigned long size, struct patch *patch)
 	return used;
 }
 
+static void prefix_one(char **name)
+{
+	char *old_name = *name;
+	if (!old_name)
+		return;
+	*name = xstrdup(prefix_filename(prefix, prefix_length, *name));
+	free(old_name);
+}
+
+static void prefix_patch(struct patch *p)
+{
+	if (!prefix || p->is_toplevel_relative)
+		return;
+	prefix_one(&p->new_name);
+	prefix_one(&p->old_name);
+}
+
 /*
- * Read the patch text in "buffer" taht extends for "size" bytes; stop
+ * include/exclude
+ */
+
+static struct string_list limit_by_name;
+static int has_include;
+static void add_name_limit(const char *name, int exclude)
+{
+	struct string_list_item *it;
+
+	it = string_list_append(&limit_by_name, name);
+	it->util = exclude ? NULL : (void *) 1;
+}
+
+static int use_patch(struct patch *p)
+{
+	const char *pathname = p->new_name ? p->new_name : p->old_name;
+	int i;
+
+	/* Paths outside are not touched regardless of "--include" */
+	if (0 < prefix_length) {
+		int pathlen = strlen(pathname);
+		if (pathlen <= prefix_length ||
+		    memcmp(prefix, pathname, prefix_length))
+			return 0;
+	}
+
+	/* See if it matches any of exclude/include rule */
+	for (i = 0; i < limit_by_name.nr; i++) {
+		struct string_list_item *it = &limit_by_name.items[i];
+		if (!wildmatch(it->string, pathname, 0, NULL))
+			return (it->util != NULL);
+	}
+
+	/*
+	 * If we had any include, a path that does not match any rule is
+	 * not used.  Otherwise, we saw bunch of exclude rules (or none)
+	 * and such a path is used.
+	 */
+	return !has_include;
+}
+
+
+/*
+ * Read the patch text in "buffer" that extends for "size" bytes; stop
  * reading after seeing a single patch (i.e. changes to a single file).
  * Create fragments (i.e. patch hunks) and hang them to the given patch.
  * Return the number of bytes consumed, so that the caller can call us
@@ -1933,21 +1996,20 @@ static int parse_chunk(char *buffer, unsigned long size, struct patch *patch)
 	if (offset < 0)
 		return offset;
 
-	patch->ws_rule = whitespace_rule(patch->new_name
-					 ? patch->new_name
-					 : patch->old_name);
+	prefix_patch(patch);
+
+	if (!use_patch(patch))
+		patch->ws_rule = 0;
+	else
+		patch->ws_rule = whitespace_rule(patch->new_name
+						 ? patch->new_name
+						 : patch->old_name);
 
 	patchsize = parse_single_patch(buffer + offset + hdrsize,
 				       size - offset - hdrsize, patch);
 
 	if (!patchsize) {
-		static const char *binhdr[] = {
-			"Binary files ",
-			"Files ",
-			NULL,
-		};
 		static const char git_binary[] = "GIT binary patch\n";
-		int i;
 		int hd = hdrsize + offset;
 		unsigned long llen = linelen(buffer + hd, size - hd);
 
@@ -1963,6 +2025,12 @@ static int parse_chunk(char *buffer, unsigned long size, struct patch *patch)
 				patchsize = 0;
 		}
 		else if (!memcmp(" differ\n", buffer + hd + llen - 8, 8)) {
+			static const char *binhdr[] = {
+				"Binary files ",
+				"Files ",
+				NULL,
+			};
+			int i;
 			for (i = 0; binhdr[i]; i++) {
 				int len = strlen(binhdr[i]);
 				if (len < size - hd &&
@@ -2095,7 +2163,7 @@ static void update_pre_post_images(struct image *preimage,
 				   char *buf,
 				   size_t len, size_t postlen)
 {
-	int i, ctx;
+	int i, ctx, reduced;
 	char *new, *old, *fixed;
 	struct image fixed_preimage;
 
@@ -2105,18 +2173,20 @@ static void update_pre_post_images(struct image *preimage,
 	 * free "oldlines".
 	 */
 	prepare_image(&fixed_preimage, buf, len, 1);
-	assert(fixed_preimage.nr == preimage->nr);
-	for (i = 0; i < preimage->nr; i++)
+	assert(postlen
+	       ? fixed_preimage.nr == preimage->nr
+	       : fixed_preimage.nr <= preimage->nr);
+	for (i = 0; i < fixed_preimage.nr; i++)
 		fixed_preimage.line[i].flag = preimage->line[i].flag;
 	free(preimage->line_allocated);
 	*preimage = fixed_preimage;
 
 	/*
 	 * Adjust the common context lines in postimage. This can be
-	 * done in-place when we are just doing whitespace fixing,
-	 * which does not make the string grow, but needs a new buffer
-	 * when ignoring whitespace causes the update, since in this case
-	 * we could have e.g. tabs converted to multiple spaces.
+	 * done in-place when we are shrinking it with whitespace
+	 * fixing, but needs a new buffer when ignoring whitespace or
+	 * expanding leading tabs to spaces.
+	 *
 	 * We trust the caller to tell us if the update can be done
 	 * in place (postlen==0) or not.
 	 */
@@ -2126,7 +2196,8 @@ static void update_pre_post_images(struct image *preimage,
 	else
 		new = old;
 	fixed = preimage->buf;
-	for (i = ctx = 0; i < postimage->nr; i++) {
+
+	for (i = reduced = ctx = 0; i < postimage->nr; i++) {
 		size_t len = postimage->line[i].len;
 		if (!(postimage->line[i].flag & LINE_COMMON)) {
 			/* an added line -- no counterparts in preimage */
@@ -2145,8 +2216,15 @@ static void update_pre_post_images(struct image *preimage,
 			fixed += preimage->line[ctx].len;
 			ctx++;
 		}
-		if (preimage->nr <= ctx)
-			die(_("oops"));
+
+		/*
+		 * preimage is expected to run out, if the caller
+		 * fixed addition of trailing blank lines.
+		 */
+		if (preimage->nr <= ctx) {
+			reduced++;
+			continue;
+		}
 
 		/* and copy it in, while fixing the line length */
 		len = preimage->line[ctx].len;
@@ -2159,6 +2237,7 @@ static void update_pre_post_images(struct image *preimage,
 
 	/* Fix the length of the whole thing */
 	postimage->len = new - postimage->buf;
+	postimage->nr -= reduced;
 }
 
 static int match_fragment(struct image *img,
@@ -2172,7 +2251,7 @@ static int match_fragment(struct image *img,
 	int i;
 	char *fixed_buf, *buf, *orig, *target;
 	struct strbuf fixed;
-	size_t fixed_len;
+	size_t fixed_len, postlen;
 	int preimage_limit;
 
 	if (preimage->nr + try_lno <= img->nr) {
@@ -2322,6 +2401,7 @@ static int match_fragment(struct image *img,
 	strbuf_init(&fixed, preimage->len + 1);
 	orig = preimage->buf;
 	target = img->buf + try;
+	postlen = 0;
 	for (i = 0; i < preimage_limit; i++) {
 		size_t oldlen = preimage->line[i].len;
 		size_t tgtlen = img->line[try_lno + i].len;
@@ -2349,6 +2429,7 @@ static int match_fragment(struct image *img,
 		match = (tgtfix.len == fixed.len - fixstart &&
 			 !memcmp(tgtfix.buf, fixed.buf + fixstart,
 					     fixed.len - fixstart));
+		postlen += tgtfix.len;
 
 		strbuf_release(&tgtfix);
 		if (!match)
@@ -2386,8 +2467,10 @@ static int match_fragment(struct image *img,
 	 * hunk match.  Update the context lines in the postimage.
 	 */
 	fixed_buf = strbuf_detach(&fixed, &fixed_len);
+	if (postlen < postimage->len)
+		postlen = 0;
 	update_pre_post_images(preimage, postimage,
-			       fixed_buf, fixed_len, 0);
+			       fixed_buf, fixed_len, postlen);
 	return 1;
 
  unmatch_exit:
@@ -2544,7 +2627,7 @@ static void update_image(struct image *img,
 		 * NOTE: this knows that we never call remove_first_line()
 		 * on anything other than pre/post image.
 		 */
-		img->line = xrealloc(img->line, nr * sizeof(*img->line));
+		REALLOC_ARRAY(img->line, nr);
 		img->line_allocated = img->line;
 	}
 	if (preimage_limit != postimage->nr)
@@ -2850,9 +2933,7 @@ static int apply_binary_fragment(struct image *img, struct patch *patch)
 	case BINARY_LITERAL_DEFLATED:
 		clear_image(img);
 		img->len = fragment->size;
-		img->buf = xmalloc(img->len+1);
-		memcpy(img->buf, fragment->patch, img->len);
-		img->buf[img->len] = '\0';
+		img->buf = xmemdupz(fragment->patch, img->len);
 		return 0;
 	}
 	return -1;
@@ -2982,7 +3063,7 @@ static int read_blob_object(struct strbuf *buf, const unsigned char *sha1, unsig
 	return 0;
 }
 
-static int read_file_or_gitlink(struct cache_entry *ce, struct strbuf *buf)
+static int read_file_or_gitlink(const struct cache_entry *ce, struct strbuf *buf)
 {
 	if (!ce)
 		return 0;
@@ -3012,7 +3093,7 @@ static struct patch *in_fn_table(const char *name)
  *
  * The latter is needed to deal with a case where two paths A and B
  * are swapped by first renaming A to B and then renaming B to A;
- * moving A to B should not be prevented due to presense of B as we
+ * moving A to B should not be prevented due to presence of B as we
  * will remove it in a later patch.
  */
 #define PATH_TO_BE_DELETED ((struct patch *) -2)
@@ -3067,13 +3148,15 @@ static void prepare_fn_table(struct patch *patch)
 	}
 }
 
-static int checkout_target(struct cache_entry *ce, struct stat *st)
+static int checkout_target(struct index_state *istate,
+			   struct cache_entry *ce, struct stat *st)
 {
 	struct checkout costate;
 
 	memset(&costate, 0, sizeof(costate));
 	costate.base_dir = "";
 	costate.refresh_cache = 1;
+	costate.istate = istate;
 	if (checkout_entry(ce, &costate, NULL) || lstat(ce->name, st))
 		return error(_("cannot checkout %s"), ce->name);
 	return 0;
@@ -3100,7 +3183,7 @@ static struct patch *previous_patch(struct patch *patch, int *gone)
 	return previous;
 }
 
-static int verify_index_match(struct cache_entry *ce, struct stat *st)
+static int verify_index_match(const struct cache_entry *ce, struct stat *st)
 {
 	if (S_ISGITLINK(ce->ce_mode)) {
 		if (!S_ISDIR(st->st_mode))
@@ -3113,7 +3196,7 @@ static int verify_index_match(struct cache_entry *ce, struct stat *st)
 #define SUBMODULE_PATCH_WITHOUT_INDEX 1
 
 static int load_patch_target(struct strbuf *buf,
-			     struct cache_entry *ce,
+			     const struct cache_entry *ce,
 			     struct stat *st,
 			     const char *name,
 			     unsigned expected_mode)
@@ -3143,7 +3226,8 @@ static int load_patch_target(struct strbuf *buf,
  * we read from the result of a previous diff.
  */
 static int load_preimage(struct image *image,
-			 struct patch *patch, struct stat *st, struct cache_entry *ce)
+			 struct patch *patch, struct stat *st,
+			 const struct cache_entry *ce)
 {
 	struct strbuf buf = STRBUF_INIT;
 	size_t len;
@@ -3239,7 +3323,7 @@ static int load_current(struct image *image, struct patch *patch)
 	if (lstat(name, &st)) {
 		if (errno != ENOENT)
 			return error(_("%s: %s"), name, strerror(errno));
-		if (checkout_target(ce, &st))
+		if (checkout_target(&the_index, ce, &st))
 			return -1;
 	}
 	if (verify_index_match(ce, &st))
@@ -3256,7 +3340,7 @@ static int load_current(struct image *image, struct patch *patch)
 }
 
 static int try_threeway(struct image *image, struct patch *patch,
-			struct stat *st, struct cache_entry *ce)
+			struct stat *st, const struct cache_entry *ce)
 {
 	unsigned char pre_sha1[20], post_sha1[20], our_sha1[20];
 	struct strbuf buf = STRBUF_INIT;
@@ -3326,7 +3410,7 @@ static int try_threeway(struct image *image, struct patch *patch,
 	return 0;
 }
 
-static int apply_data(struct patch *patch, struct stat *st, struct cache_entry *ce)
+static int apply_data(struct patch *patch, struct stat *st, const struct cache_entry *ce)
 {
 	struct image image;
 
@@ -3393,7 +3477,7 @@ static int check_preimage(struct patch *patch, struct cache_entry **ce, struct s
 		}
 		*ce = active_cache[pos];
 		if (stat_ret < 0) {
-			if (checkout_target(*ce, st))
+			if (checkout_target(&the_index, *ce, st))
 				return -1;
 		}
 		if (!cached && verify_index_match(*ce, st))
@@ -3496,7 +3580,7 @@ static int check_patch(struct patch *patch)
 	 *
 	 * A patch to swap-rename between A and B would first rename A
 	 * to B and then rename B to A.  While applying the first one,
-	 * the presense of B should not stop A from getting renamed to
+	 * the presence of B should not stop A from getting renamed to
 	 * B; ask to_be_deleted() about the later rename.  Removal of
 	 * B and rename from A to B is handled the same way by asking
 	 * was_deleted().
@@ -3508,7 +3592,7 @@ static int check_patch(struct patch *patch)
 		ok_if_exists = 0;
 
 	if (new_name &&
-	    ((0 < patch->is_new) | (0 < patch->is_rename) | patch->is_copy)) {
+	    ((0 < patch->is_new) || patch->is_rename || patch->is_copy)) {
 		int err = check_to_create(new_name, ok_if_exists);
 
 		if (err && threeway) {
@@ -3587,18 +3671,51 @@ static int get_current_sha1(const char *path, unsigned char *sha1)
 	return 0;
 }
 
+static int preimage_sha1_in_gitlink_patch(struct patch *p, unsigned char sha1[20])
+{
+	/*
+	 * A usable gitlink patch has only one fragment (hunk) that looks like:
+	 * @@ -1 +1 @@
+	 * -Subproject commit <old sha1>
+	 * +Subproject commit <new sha1>
+	 * or
+	 * @@ -1 +0,0 @@
+	 * -Subproject commit <old sha1>
+	 * for a removal patch.
+	 */
+	struct fragment *hunk = p->fragments;
+	static const char heading[] = "-Subproject commit ";
+	char *preimage;
+
+	if (/* does the patch have only one hunk? */
+	    hunk && !hunk->next &&
+	    /* is its preimage one line? */
+	    hunk->oldpos == 1 && hunk->oldlines == 1 &&
+	    /* does preimage begin with the heading? */
+	    (preimage = memchr(hunk->patch, '\n', hunk->size)) != NULL &&
+	    starts_with(++preimage, heading) &&
+	    /* does it record full SHA-1? */
+	    !get_sha1_hex(preimage + sizeof(heading) - 1, sha1) &&
+	    preimage[sizeof(heading) + 40 - 1] == '\n' &&
+	    /* does the abbreviated name on the index line agree with it? */
+	    starts_with(preimage + sizeof(heading) - 1, p->old_sha1_prefix))
+		return 0; /* it all looks fine */
+
+	/* we may have full object name on the index line */
+	return get_sha1_hex(p->old_sha1_prefix, sha1);
+}
+
 /* Build an index that contains the just the files needed for a 3way merge */
 static void build_fake_ancestor(struct patch *list, const char *filename)
 {
 	struct patch *patch;
 	struct index_state result = { NULL };
-	int fd;
+	static struct lock_file lock;
 
 	/* Once we start supporting the reverse patch, it may be
 	 * worth showing the new sha1 prefix, but until then...
 	 */
 	for (patch = list; patch; patch = patch->next) {
-		const unsigned char *sha1_ptr;
 		unsigned char sha1[20];
 		struct cache_entry *ce;
 		const char *name;
@@ -3606,28 +3723,33 @@ static void build_fake_ancestor(struct patch *list, const char *filename)
 		name = patch->old_name ? patch->old_name : patch->new_name;
 		if (0 < patch->is_new)
 			continue;
-		else if (get_sha1_blob(patch->old_sha1_prefix, sha1))
-			/* git diff has no index line for mode/type changes */
-			if (!patch->lines_added && !patch->lines_deleted) {
-				if (get_current_sha1(patch->old_name, sha1))
-					die("mode change for %s, which is not "
-						"in current HEAD", name);
-				sha1_ptr = sha1;
-			} else
-				die("sha1 information is lacking or useless "
-					"(%s).", name);
-		else
-			sha1_ptr = sha1;
 
-		ce = make_cache_entry(patch->old_mode, sha1_ptr, name, 0, 0);
+		if (S_ISGITLINK(patch->old_mode)) {
+			if (!preimage_sha1_in_gitlink_patch(patch, sha1))
+				; /* ok, the textual part looks sane */
+			else
+				die("sha1 information is lacking or useless for submodule %s",
+				    name);
+		} else if (!get_sha1_blob(patch->old_sha1_prefix, sha1)) {
+			; /* ok */
+		} else if (!patch->lines_added && !patch->lines_deleted) {
+			/* mode-only change: update the current */
+			if (get_current_sha1(patch->old_name, sha1))
+				die("mode change for %s, which is not "
+				    "in current HEAD", name);
+		} else
+			die("sha1 information is lacking or useless "
+			    "(%s).", name);
+
+		ce = make_cache_entry(patch->old_mode, sha1, name, 0, 0);
 		if (!ce)
 			die(_("make_cache_entry failed for path '%s'"), name);
 		if (add_index_entry(&result, ce, ADD_CACHE_OK_TO_ADD))
 			die ("Could not add %s to temporary index", name);
 	}
 
-	fd = open(filename, O_WRONLY | O_CREAT, 0666);
-	if (fd < 0 || write_index(&result, fd) || close(fd))
+	hold_lock_file_for_update(&lock, filename, LOCK_DIE_ON_ERROR);
+	if (write_locked_index(&result, &lock, COMMIT_LOCK))
 		die ("Could not write temporary index to %s", filename);
 
 	discard_index(&result);
@@ -3789,10 +3911,11 @@ static void add_index_file(const char *path, unsigned mode, void *buf, unsigned
 	ce->ce_flags = create_ce_flags(0);
 	ce->ce_namelen = namelen;
 	if (S_ISGITLINK(mode)) {
-		const char *s = buf;
+		const char *s;
 
-		if (get_sha1_hex(s + strlen("Subproject commit "), ce->sha1))
-			die(_("corrupt patch for subproject %s"), path);
+		if (!skip_prefix(buf, "Subproject commit ", &s) ||
+		    get_sha1_hex(s, ce->sha1))
+			die(_("corrupt patch for submodule %s"), path);
 	} else {
 		if (!cached) {
 			if (lstat(path, &st) < 0)
@@ -4005,7 +4128,7 @@ static int write_out_one_reject(struct patch *patch)
 		return error(_("cannot open %s: %s"), namebuf, strerror(errno));
 
 	/* Normal git tools never deal with .rej, so do not pretend
-	 * this is a git patch by saying --git nor give extended
+	 * this is a git patch by saying --git or giving extended
 	 * headers.  While at it, maybe please "kompare" that wants
 	 * the trailing TAB and some garbage at the end of line ;-).
 	 */
@@ -4057,7 +4180,7 @@ static int write_out_results(struct patch *list)
 	if (cpath.nr) {
 		struct string_list_item *item;
 
-		sort_string_list(&cpath);
+		string_list_sort(&cpath);
 		for_each_string_list_item(item, &cpath)
 			fprintf(stderr, "U %s\n", item->string);
 		string_list_clear(&cpath, 0);
@@ -4070,64 +4193,6 @@ static int write_out_results(struct patch *list)
 
 static struct lock_file lock_file;
 
-static struct string_list limit_by_name;
-static int has_include;
-static void add_name_limit(const char *name, int exclude)
-{
-	struct string_list_item *it;
-
-	it = string_list_append(&limit_by_name, name);
-	it->util = exclude ? NULL : (void *) 1;
-}
-
-static int use_patch(struct patch *p)
-{
-	const char *pathname = p->new_name ? p->new_name : p->old_name;
-	int i;
-
-	/* Paths outside are not touched regardless of "--include" */
-	if (0 < prefix_length) {
-		int pathlen = strlen(pathname);
-		if (pathlen <= prefix_length ||
-		    memcmp(prefix, pathname, prefix_length))
-			return 0;
-	}
-
-	/* See if it matches any of exclude/include rule */
-	for (i = 0; i < limit_by_name.nr; i++) {
-		struct string_list_item *it = &limit_by_name.items[i];
-		if (!fnmatch(it->string, pathname, 0))
-			return (it->util != NULL);
-	}
-
-	/*
-	 * If we had any include, a path that does not match any rule is
-	 * not used.  Otherwise, we saw bunch of exclude rules (or none)
-	 * and such a path is used.
-	 */
-	return !has_include;
-}
-
-
-static void prefix_one(char **name)
-{
-	char *old_name = *name;
-	if (!old_name)
-		return;
-	*name = xstrdup(prefix_filename(prefix, prefix_length, *name));
-	free(old_name);
-}
-
-static void prefix_patches(struct patch *p)
-{
-	if (!prefix || p->is_toplevel_relative)
-		return;
-	for ( ; p; p = p->next) {
-		prefix_one(&p->new_name);
-		prefix_one(&p->old_name);
-	}
-}
-
 #define INACCURATE_EOF	(1<<0)
 #define RECOUNT		(1<<1)
 
@@ -4153,8 +4218,6 @@ static int apply_patch(int fd, const char *filename, int options)
 			break;
 		if (apply_in_reverse)
 			reverse_patches(patch);
-		if (prefix)
-			prefix_patches(patch);
 		if (use_patch(patch)) {
 			patch_stats(patch);
 			*listp = patch;
@@ -4212,13 +4275,11 @@ static int apply_patch(int fd, const char *filename, int options)
 	return 0;
 }
 
-static int git_apply_config(const char *var, const char *value, void *cb)
+static void git_apply_config(void)
 {
-	if (!strcmp(var, "apply.whitespace"))
-		return git_config_string(&apply_default_whitespace, var, value);
-	else if (!strcmp(var, "apply.ignorewhitespace"))
-		return git_config_string(&apply_default_ignorewhitespace, var, value);
-	return git_default_config(var, value, cb);
+	git_config_get_string_const("apply.whitespace", &apply_default_whitespace);
+	git_config_get_string_const("apply.ignorewhitespace", &apply_default_ignorewhitespace);
+	git_config(git_default_config, NULL);
 }
 
 static int option_parse_exclude(const struct option *opt,
@@ -4307,23 +4368,23 @@ int cmd_apply(int argc, const char **argv, const char *prefix_)
 		{ OPTION_CALLBACK, 'p', NULL, NULL, N_("num"),
 			N_("remove <num> leading slashes from traditional diff paths"),
 			0, option_parse_p },
-		OPT_BOOLEAN(0, "no-add", &no_add,
+		OPT_BOOL(0, "no-add", &no_add,
 			N_("ignore additions made by the patch")),
-		OPT_BOOLEAN(0, "stat", &diffstat,
+		OPT_BOOL(0, "stat", &diffstat,
 			N_("instead of applying the patch, output diffstat for the input")),
 		OPT_NOOP_NOARG(0, "allow-binary-replacement"),
 		OPT_NOOP_NOARG(0, "binary"),
-		OPT_BOOLEAN(0, "numstat", &numstat,
+		OPT_BOOL(0, "numstat", &numstat,
 			N_("show number of added and deleted lines in decimal notation")),
-		OPT_BOOLEAN(0, "summary", &summary,
+		OPT_BOOL(0, "summary", &summary,
 			N_("instead of applying the patch, output a summary for the input")),
-		OPT_BOOLEAN(0, "check", &check,
+		OPT_BOOL(0, "check", &check,
 			N_("instead of applying the patch, see if the patch is applicable")),
-		OPT_BOOLEAN(0, "index", &check_index,
+		OPT_BOOL(0, "index", &check_index,
 			N_("make sure the patch is applicable to the current index")),
-		OPT_BOOLEAN(0, "cached", &cached,
+		OPT_BOOL(0, "cached", &cached,
 			N_("apply a patch without touching the working tree")),
-		OPT_BOOLEAN(0, "apply", &force_apply,
+		OPT_BOOL(0, "apply", &force_apply,
 			N_("also apply the patch (use with --stat/--summary/--check)")),
 		OPT_BOOL('3', "3way", &threeway,
 			 N_( "attempt three-way merge if a patch does not apply")),
@@ -4343,13 +4404,13 @@ int cmd_apply(int argc, const char **argv, const char *prefix_)
 		{ OPTION_CALLBACK, 0, "ignore-whitespace", NULL, NULL,
 			N_("ignore changes in whitespace when finding context"),
 			PARSE_OPT_NOARG, option_parse_space_change },
-		OPT_BOOLEAN('R', "reverse", &apply_in_reverse,
+		OPT_BOOL('R', "reverse", &apply_in_reverse,
 			N_("apply the patch in reverse")),
-		OPT_BOOLEAN(0, "unidiff-zero", &unidiff_zero,
+		OPT_BOOL(0, "unidiff-zero", &unidiff_zero,
 			N_("don't expect at least one line of context")),
-		OPT_BOOLEAN(0, "reject", &apply_with_reject,
+		OPT_BOOL(0, "reject", &apply_with_reject,
 			N_("leave the rejected hunks in corresponding *.rej files")),
-		OPT_BOOLEAN(0, "allow-overlap", &allow_overlap,
+		OPT_BOOL(0, "allow-overlap", &allow_overlap,
 			N_("allow overlapping hunks")),
 		OPT__VERBOSE(&apply_verbosely, N_("be verbose")),
 		OPT_BIT(0, "inaccurate-eof", &options,
@@ -4366,7 +4427,7 @@ int cmd_apply(int argc, const char **argv, const char *prefix_)
 
 	prefix = prefix_;
 	prefix_length = prefix ? strlen(prefix) : 0;
-	git_config(git_apply_config, NULL);
+	git_apply_config();
 	if (apply_default_whitespace)
 		parse_whitespace_option(apply_default_whitespace);
 	if (apply_default_ignorewhitespace)
@@ -4445,8 +4506,7 @@ int cmd_apply(int argc, const char **argv, const char *prefix_)
 	}
 
 	if (update_index) {
-		if (write_cache(newfd, active_cache, active_nr) ||
-		    commit_locked_index(&lock_file))
+		if (write_locked_index(&the_index, &lock_file, COMMIT_LOCK))
 			die(_("Unable to write new index file"));
 	}