diff --git a/Makefile b/Makefile
index 865e2bfcf1..f08d5f7bed 100644
--- a/Makefile
+++ b/Makefile
@@ -235,7 +235,6 @@ BASIC_LDFLAGS =
 
 SCRIPT_SH += git-am.sh
 SCRIPT_SH += git-bisect.sh
-SCRIPT_SH += git-clone.sh
 SCRIPT_SH += git-filter-branch.sh
 SCRIPT_SH += git-lost-found.sh
 SCRIPT_SH += git-merge-octopus.sh
@@ -484,6 +483,7 @@ BUILTIN_OBJS += builtin-check-ref-format.o
 BUILTIN_OBJS += builtin-checkout-index.o
 BUILTIN_OBJS += builtin-checkout.o
 BUILTIN_OBJS += builtin-clean.o
+BUILTIN_OBJS += builtin-clone.o
 BUILTIN_OBJS += builtin-commit-tree.o
 BUILTIN_OBJS += builtin-commit.o
 BUILTIN_OBJS += builtin-config.o
diff --git a/builtin-clone.c b/builtin-clone.c
new file mode 100644
index 0000000000..2a3f6732f2
--- /dev/null
+++ b/builtin-clone.c
@@ -0,0 +1,550 @@
+/*
+ * Builtin "git clone"
+ *
+ * Copyright (c) 2007 Kristian Høgsberg <krh@redhat.com>,
+ *		 2008 Daniel Barkalow <barkalow@iabervon.org>
+ * Based on git-commit.sh by Junio C Hamano and Linus Torvalds
+ *
+ * Clone a repository into a different directory that does not yet exist.
+ */
+
+#include "cache.h"
+#include "parse-options.h"
+#include "fetch-pack.h"
+#include "refs.h"
+#include "tree.h"
+#include "tree-walk.h"
+#include "unpack-trees.h"
+#include "transport.h"
+#include "strbuf.h"
+#include "dir.h"
+
+/*
+ * Overall FIXMEs:
+ *  - respect DB_ENVIRONMENT for .git/objects.
+ *
+ * Implementation notes:
+ *  - dropping use-separate-remote and no-separate-remote compatibility
+ *
+ */
+static const char * const builtin_clone_usage[] = {
+	"git-clone [options] [--] <repo> [<dir>]",
+	NULL
+};
+
+static int option_quiet, option_no_checkout, option_bare;
+static int option_local, option_no_hardlinks, option_shared;
+static char *option_template, *option_reference, *option_depth;
+static char *option_origin = NULL;
+static char *option_upload_pack = "git-upload-pack";
+
+static struct option builtin_clone_options[] = {
+	OPT__QUIET(&option_quiet),
+	OPT_BOOLEAN('n', "no-checkout", &option_no_checkout,
+		    "don't create a checkout"),
+	OPT_BOOLEAN(0, "bare", &option_bare, "create a bare repository"),
+	OPT_BOOLEAN(0, "naked", &option_bare, "create a bare repository"),
+	OPT_BOOLEAN('l', "local", &option_local,
+		    "to clone from a local repository"),
+	OPT_BOOLEAN(0, "no-hardlinks", &option_no_hardlinks,
+		    "don't use local hardlinks, always copy"),
+	OPT_BOOLEAN('s', "shared", &option_shared,
+		    "setup as shared repository"),
+	OPT_STRING(0, "template", &option_template, "path",
+		   "path the template repository"),
+	OPT_STRING(0, "reference", &option_reference, "repo",
+		   "reference repository"),
+	OPT_STRING('o', "origin", &option_origin, "branch",
+		   "use <branch> instead or 'origin' to track upstream"),
+	OPT_STRING('u', "upload-pack", &option_upload_pack, "path",
+		   "path to git-upload-pack on the remote"),
+	OPT_STRING(0, "depth", &option_depth, "depth",
+		    "create a shallow clone of that depth"),
+
+	OPT_END()
+};
+
+static char *get_repo_path(const char *repo, int *is_bundle)
+{
+	static char *suffix[] = { "/.git", ".git", "" };
+	static char *bundle_suffix[] = { ".bundle", "" };
+	struct stat st;
+	int i;
+
+	for (i = 0; i < ARRAY_SIZE(suffix); i++) {
+		const char *path;
+		path = mkpath("%s%s", repo, suffix[i]);
+		if (!stat(path, &st) && S_ISDIR(st.st_mode)) {
+			*is_bundle = 0;
+			return xstrdup(make_absolute_path(path));
+		}
+	}
+
+	for (i = 0; i < ARRAY_SIZE(bundle_suffix); i++) {
+		const char *path;
+		path = mkpath("%s%s", repo, bundle_suffix[i]);
+		if (!stat(path, &st) && S_ISREG(st.st_mode)) {
+			*is_bundle = 1;
+			return xstrdup(make_absolute_path(path));
+		}
+	}
+
+	return NULL;
+}
+
+static char *guess_dir_name(const char *repo, int is_bundle)
+{
+	const char *p, *start, *end, *limit;
+	int after_slash_or_colon;
+
+	/* Guess dir name from repository: strip trailing '/',
+	 * strip trailing '[:/]*.{git,bundle}', strip leading '.*[/:]'. */
+
+	after_slash_or_colon = 1;
+	limit = repo + strlen(repo);
+	start = repo;
+	end = limit;
+	for (p = repo; p < limit; p++) {
+		const char *prefix = is_bundle ? ".bundle" : ".git";
+		if (!prefixcmp(p, prefix)) {
+			if (!after_slash_or_colon)
+				end = p;
+			p += strlen(prefix) - 1;
+		} else if (!prefixcmp(p, ".bundle")) {
+			if (!after_slash_or_colon)
+				end = p;
+			p += 7;
+		} else if (*p == '/' || *p == ':') {
+			if (end == limit)
+				end = p;
+			after_slash_or_colon = 1;
+		} else if (after_slash_or_colon) {
+			start = p;
+			end = limit;
+			after_slash_or_colon = 0;
+		}
+	}
+
+	return xstrndup(start, end - start);
+}
+
+static int is_directory(const char *path)
+{
+	struct stat buf;
+
+	return !stat(path, &buf) && S_ISDIR(buf.st_mode);
+}
+
+static void setup_reference(const char *repo)
+{
+	const char *ref_git;
+	char *ref_git_copy;
+
+	struct remote *remote;
+	struct transport *transport;
+	const struct ref *extra;
+
+	ref_git = make_absolute_path(option_reference);
+
+	if (is_directory(mkpath("%s/.git/objects", ref_git)))
+		ref_git = mkpath("%s/.git", ref_git);
+	else if (!is_directory(mkpath("%s/objects", ref_git)))
+		die("reference repository '%s' is not a local directory.",
+		    option_reference);
+
+	ref_git_copy = xstrdup(ref_git);
+
+	add_to_alternates_file(ref_git_copy);
+
+	remote = remote_get(ref_git_copy);
+	transport = transport_get(remote, ref_git_copy);
+	for (extra = transport_get_remote_refs(transport); extra;
+	     extra = extra->next)
+		add_extra_ref(extra->name, extra->old_sha1, 0);
+
+	transport_disconnect(transport);
+
+	free(ref_git_copy);
+}
+
+static void copy_or_link_directory(char *src, char *dest)
+{
+	struct dirent *de;
+	struct stat buf;
+	int src_len, dest_len;
+	DIR *dir;
+
+	dir = opendir(src);
+	if (!dir)
+		die("failed to open %s\n", src);
+
+	if (mkdir(dest, 0777)) {
+		if (errno != EEXIST)
+			die("failed to create directory %s\n", dest);
+		else if (stat(dest, &buf))
+			die("failed to stat %s\n", dest);
+		else if (!S_ISDIR(buf.st_mode))
+			die("%s exists and is not a directory\n", dest);
+	}
+
+	src_len = strlen(src);
+	src[src_len] = '/';
+	dest_len = strlen(dest);
+	dest[dest_len] = '/';
+
+	while ((de = readdir(dir)) != NULL) {
+		strcpy(src + src_len + 1, de->d_name);
+		strcpy(dest + dest_len + 1, de->d_name);
+		if (stat(src, &buf)) {
+			warning ("failed to stat %s\n", src);
+			continue;
+		}
+		if (S_ISDIR(buf.st_mode)) {
+			if (de->d_name[0] != '.')
+				copy_or_link_directory(src, dest);
+			continue;
+		}
+
+		if (unlink(dest) && errno != ENOENT)
+			die("failed to unlink %s\n", dest);
+		if (!option_no_hardlinks) {
+			if (!link(src, dest))
+				continue;
+			if (option_local)
+				die("failed to create link %s\n", dest);
+			option_no_hardlinks = 1;
+		}
+		if (copy_file(dest, src, 0666))
+			die("failed to copy file to %s\n", dest);
+	}
+	closedir(dir);
+}
+
+static const struct ref *clone_local(const char *src_repo,
+				     const char *dest_repo)
+{
+	const struct ref *ret;
+	char src[PATH_MAX];
+	char dest[PATH_MAX];
+	struct remote *remote;
+	struct transport *transport;
+
+	if (option_shared)
+		add_to_alternates_file(src_repo);
+	else {
+		snprintf(src, PATH_MAX, "%s/objects", src_repo);
+		snprintf(dest, PATH_MAX, "%s/objects", dest_repo);
+		copy_or_link_directory(src, dest);
+	}
+
+	remote = remote_get(src_repo);
+	transport = transport_get(remote, src_repo);
+	ret = transport_get_remote_refs(transport);
+	transport_disconnect(transport);
+	return ret;
+}
+
+static const char *junk_work_tree;
+static const char *junk_git_dir;
+pid_t junk_pid;
+
+static void remove_junk(void)
+{
+	struct strbuf sb;
+	if (getpid() != junk_pid)
+		return;
+	strbuf_init(&sb, 0);
+	if (junk_git_dir) {
+		strbuf_addstr(&sb, junk_git_dir);
+		remove_dir_recursively(&sb, 0);
+		strbuf_reset(&sb);
+	}
+	if (junk_work_tree) {
+		strbuf_addstr(&sb, junk_work_tree);
+		remove_dir_recursively(&sb, 0);
+		strbuf_reset(&sb);
+	}
+}
+
+static void remove_junk_on_signal(int signo)
+{
+	remove_junk();
+	signal(SIGINT, SIG_DFL);
+	raise(signo);
+}
+
+static const struct ref *locate_head(const struct ref *refs,
+				     const struct ref *mapped_refs,
+				     const struct ref **remote_head_p)
+{
+	const struct ref *remote_head = NULL;
+	const struct ref *remote_master = NULL;
+	const struct ref *r;
+	for (r = refs; r; r = r->next)
+		if (!strcmp(r->name, "HEAD"))
+			remote_head = r;
+
+	for (r = mapped_refs; r; r = r->next)
+		if (!strcmp(r->name, "refs/heads/master"))
+			remote_master = r;
+
+	if (remote_head_p)
+		*remote_head_p = remote_head;
+
+	/* If there's no HEAD value at all, never mind. */
+	if (!remote_head)
+		return NULL;
+
+	/* If refs/heads/master could be right, it is. */
+	if (remote_master && !hashcmp(remote_master->old_sha1,
+				      remote_head->old_sha1))
+		return remote_master;
+
+	/* Look for another ref that points there */
+	for (r = mapped_refs; r; r = r->next)
+		if (r != remote_head &&
+		    !hashcmp(r->old_sha1, remote_head->old_sha1))
+			return r;
+
+	/* Nothing is the same */
+	return NULL;
+}
+
+static struct ref *write_remote_refs(const struct ref *refs,
+		struct refspec *refspec, const char *reflog)
+{
+	struct ref *local_refs = NULL;
+	struct ref **tail = &local_refs;
+	struct ref *r;
+
+	get_fetch_map(refs, refspec, &tail, 0);
+	get_fetch_map(refs, tag_refspec, &tail, 0);
+
+	for (r = local_refs; r; r = r->next)
+		update_ref(reflog,
+			   r->peer_ref->name, r->old_sha1, NULL, 0, DIE_ON_ERR);
+	return local_refs;
+}
+
+int cmd_clone(int argc, const char **argv, const char *prefix)
+{
+	int use_local_hardlinks = 1;
+	int use_separate_remote = 1;
+	int is_bundle = 0;
+	struct stat buf;
+	const char *repo_name, *repo, *work_tree, *git_dir;
+	char *path, *dir;
+	const struct ref *refs, *head_points_at, *remote_head, *mapped_refs;
+	char branch_top[256], key[256], value[256];
+	struct strbuf reflog_msg;
+
+	struct refspec refspec;
+
+	junk_pid = getpid();
+
+	argc = parse_options(argc, argv, builtin_clone_options,
+			     builtin_clone_usage, 0);
+
+	if (argc == 0)
+		die("You must specify a repository to clone.");
+
+	if (option_no_hardlinks)
+		use_local_hardlinks = 0;
+
+	if (option_bare) {
+		if (option_origin)
+			die("--bare and --origin %s options are incompatible.",
+			    option_origin);
+		option_no_checkout = 1;
+		use_separate_remote = 0;
+	}
+
+	if (!option_origin)
+		option_origin = "origin";
+
+	repo_name = argv[0];
+
+	path = get_repo_path(repo_name, &is_bundle);
+	if (path)
+		repo = path;
+	else if (!strchr(repo_name, ':'))
+		repo = xstrdup(make_absolute_path(repo_name));
+	else
+		repo = repo_name;
+
+	if (argc == 2)
+		dir = xstrdup(argv[1]);
+	else
+		dir = guess_dir_name(repo_name, is_bundle);
+
+	if (!stat(dir, &buf))
+		die("destination directory '%s' already exists.", dir);
+
+	strbuf_init(&reflog_msg, 0);
+	strbuf_addf(&reflog_msg, "clone: from %s", repo);
+
+	if (option_bare)
+		work_tree = NULL;
+	else {
+		work_tree = getenv("GIT_WORK_TREE");
+		if (work_tree && !stat(work_tree, &buf))
+			die("working tree '%s' already exists.", work_tree);
+	}
+
+	if (option_bare || work_tree)
+		git_dir = xstrdup(dir);
+	else {
+		work_tree = dir;
+		git_dir = xstrdup(mkpath("%s/.git", dir));
+	}
+
+	if (!option_bare) {
+		junk_work_tree = work_tree;
+		if (mkdir(work_tree, 0755))
+			die("could not create work tree dir '%s'.", work_tree);
+		set_git_work_tree(work_tree);
+	}
+	junk_git_dir = git_dir;
+	atexit(remove_junk);
+	signal(SIGINT, remove_junk_on_signal);
+
+	setenv(CONFIG_ENVIRONMENT, xstrdup(mkpath("%s/config", git_dir)), 1);
+
+	set_git_dir(make_absolute_path(git_dir));
+
+	fprintf(stderr, "Initialize %s\n", git_dir);
+	init_db(option_template, option_quiet ? INIT_DB_QUIET : 0);
+
+	if (option_reference)
+		setup_reference(git_dir);
+
+	git_config(git_default_config);
+
+	if (option_bare) {
+		strcpy(branch_top, "refs/heads/");
+
+		git_config_set("core.bare", "true");
+	} else {
+		snprintf(branch_top, sizeof(branch_top),
+			 "refs/remotes/%s/", option_origin);
+
+		/* Configure the remote */
+		snprintf(key, sizeof(key), "remote.%s.url", option_origin);
+		git_config_set(key, repo);
+
+		snprintf(key, sizeof(key), "remote.%s.fetch", option_origin);
+		snprintf(value, sizeof(value),
+				"+refs/heads/*:%s*", branch_top);
+		git_config_set_multivar(key, value, "^$", 0);
+	}
+
+	refspec.force = 0;
+	refspec.pattern = 1;
+	refspec.src = "refs/heads/";
+	refspec.dst = branch_top;
+
+	if (path && !is_bundle)
+		refs = clone_local(path, git_dir);
+	else {
+		struct remote *remote = remote_get(argv[0]);
+		struct transport *transport = transport_get(remote, argv[0]);
+
+		transport_set_option(transport, TRANS_OPT_KEEP, "yes");
+
+		if (option_depth)
+			transport_set_option(transport, TRANS_OPT_DEPTH,
+					     option_depth);
+
+		if (option_quiet)
+			transport->verbose = -1;
+
+		refs = transport_get_remote_refs(transport);
+		transport_fetch_refs(transport, refs);
+	}
+
+	clear_extra_refs();
+
+	mapped_refs = write_remote_refs(refs, &refspec, reflog_msg.buf);
+
+	head_points_at = locate_head(refs, mapped_refs, &remote_head);
+
+	if (head_points_at) {
+		/* Local default branch link */
+		create_symref("HEAD", head_points_at->name, NULL);
+
+		if (!option_bare) {
+			struct strbuf head_ref;
+			const char *head = head_points_at->name;
+
+			if (!prefixcmp(head, "refs/heads/"))
+				head += 11;
+
+			/* Set up the initial local branch */
+
+			/* Local branch initial value */
+			update_ref(reflog_msg.buf, "HEAD",
+				   head_points_at->old_sha1,
+				   NULL, 0, DIE_ON_ERR);
+
+			strbuf_init(&head_ref, 0);
+			strbuf_addstr(&head_ref, branch_top);
+			strbuf_addstr(&head_ref, "HEAD");
+
+			/* Remote branch link */
+			create_symref(head_ref.buf,
+				      head_points_at->peer_ref->name,
+				      reflog_msg.buf);
+
+			snprintf(key, sizeof(key), "branch.%s.remote", head);
+			git_config_set(key, option_origin);
+			snprintf(key, sizeof(key), "branch.%s.merge", head);
+			git_config_set(key, head_points_at->name);
+		}
+	} else if (remote_head) {
+		/* Source had detached HEAD pointing somewhere. */
+		if (!option_bare)
+			update_ref(reflog_msg.buf, "HEAD",
+				   remote_head->old_sha1,
+				   NULL, REF_NODEREF, DIE_ON_ERR);
+	} else {
+		/* Nothing to checkout out */
+		if (!option_no_checkout)
+			warning("remote HEAD refers to nonexistent ref, "
+				"unable to checkout.\n");
+		option_no_checkout = 1;
+	}
+
+	if (!option_no_checkout) {
+		struct lock_file *lock_file = xcalloc(1, sizeof(struct lock_file));
+		struct unpack_trees_options opts;
+		struct tree *tree;
+		struct tree_desc t;
+		int fd;
+
+		/* We need to be in the new work tree for the checkout */
+		setup_work_tree();
+
+		fd = hold_locked_index(lock_file, 1);
+
+		memset(&opts, 0, sizeof opts);
+		opts.update = 1;
+		opts.merge = 1;
+		opts.fn = oneway_merge;
+		opts.verbose_update = !option_quiet;
+		opts.src_index = &the_index;
+		opts.dst_index = &the_index;
+
+		tree = parse_tree_indirect(remote_head->old_sha1);
+		parse_tree(tree);
+		init_tree_desc(&t, tree->buffer, tree->size);
+		unpack_trees(1, &t, &opts);
+
+		if (write_cache(fd, active_cache, active_nr) ||
+		    commit_locked_index(lock_file))
+			die("unable to write new index file");
+	}
+
+	strbuf_release(&reflog_msg);
+	junk_pid = 0;
+	return 0;
+}
diff --git a/builtin-fetch.c b/builtin-fetch.c
index f6584ecea1..bfe7711aa8 100644
--- a/builtin-fetch.c
+++ b/builtin-fetch.c
@@ -127,14 +127,8 @@ static struct ref *get_ref_map(struct transport *transport,
 		/* Merge everything on the command line, but not --tags */
 		for (rm = ref_map; rm; rm = rm->next)
 			rm->merge = 1;
-		if (tags == TAGS_SET) {
-			struct refspec refspec;
-			refspec.src = "refs/tags/";
-			refspec.dst = "refs/tags/";
-			refspec.pattern = 1;
-			refspec.force = 0;
-			get_fetch_map(remote_refs, &refspec, &tail, 0);
-		}
+		if (tags == TAGS_SET)
+			get_fetch_map(remote_refs, tag_refspec, &tail, 0);
 	} else {
 		/* Use the defaults */
 		struct remote *remote = transport->remote;
diff --git a/builtin-init-db.c b/builtin-init-db.c
index b061317275..3968c9911f 100644
--- a/builtin-init-db.c
+++ b/builtin-init-db.c
@@ -104,12 +104,14 @@ static void copy_templates_1(char *path, int baselen,
 	}
 }
 
-static void copy_templates(const char *git_dir, int len, const char *template_dir)
+static void copy_templates(const char *template_dir)
 {
 	char path[PATH_MAX];
 	char template_path[PATH_MAX];
 	int template_len;
 	DIR *dir;
+	const char *git_dir = get_git_dir();
+	int len = strlen(git_dir);
 
 	if (!template_dir)
 		template_dir = getenv(TEMPLATE_DIR_ENVIRONMENT);
@@ -156,6 +158,8 @@ static void copy_templates(const char *git_dir, int len, const char *template_di
 	}
 
 	memcpy(path, git_dir, len);
+	if (len && path[len - 1] != '/')
+		path[len++] = '/';
 	path[len] = 0;
 	copy_templates_1(path, len,
 			 template_path, template_len,
@@ -163,8 +167,9 @@ static void copy_templates(const char *git_dir, int len, const char *template_di
 	closedir(dir);
 }
 
-static int create_default_files(const char *git_dir, const char *template_path)
+static int create_default_files(const char *template_path)
 {
+	const char *git_dir = get_git_dir();
 	unsigned len = strlen(git_dir);
 	static char path[PATH_MAX];
 	struct stat st1;
@@ -183,19 +188,15 @@ static int create_default_files(const char *git_dir, const char *template_path)
 	/*
 	 * Create .git/refs/{heads,tags}
 	 */
-	strcpy(path + len, "refs");
-	safe_create_dir(path, 1);
-	strcpy(path + len, "refs/heads");
-	safe_create_dir(path, 1);
-	strcpy(path + len, "refs/tags");
-	safe_create_dir(path, 1);
+	safe_create_dir(git_path("refs"), 1);
+	safe_create_dir(git_path("refs/heads"), 1);
+	safe_create_dir(git_path("refs/tags"), 1);
 
 	/* First copy the templates -- we might have the default
 	 * config file there, in which case we would want to read
 	 * from it after installing.
 	 */
-	path[len] = 0;
-	copy_templates(path, len, template_path);
+	copy_templates(template_path);
 
 	git_config(git_default_config);
 
@@ -204,14 +205,10 @@ static int create_default_files(const char *git_dir, const char *template_path)
 	 * shared-repository settings, we would need to fix them up.
 	 */
 	if (shared_repository) {
-		path[len] = 0;
-		adjust_shared_perm(path);
-		strcpy(path + len, "refs");
-		adjust_shared_perm(path);
-		strcpy(path + len, "refs/heads");
-		adjust_shared_perm(path);
-		strcpy(path + len, "refs/tags");
-		adjust_shared_perm(path);
+		adjust_shared_perm(get_git_dir());
+		adjust_shared_perm(git_path("refs"));
+		adjust_shared_perm(git_path("refs/heads"));
+		adjust_shared_perm(git_path("refs/tags"));
 	}
 
 	/*
@@ -251,8 +248,10 @@ static int create_default_files(const char *git_dir, const char *template_path)
 		/* allow template config file to override the default */
 		if (log_all_ref_updates == -1)
 		    git_config_set("core.logallrefupdates", "true");
-		if (work_tree != git_work_tree_cfg)
+		if (prefixcmp(git_dir, work_tree) ||
+		    strcmp(git_dir + strlen(work_tree), "/.git")) {
 			git_config_set("core.worktree", work_tree);
+		}
 	}
 
 	if (!reinit) {
@@ -278,106 +277,13 @@ static int create_default_files(const char *git_dir, const char *template_path)
 	return reinit;
 }
 
-static void guess_repository_type(const char *git_dir)
+int init_db(const char *template_dir, unsigned int flags)
 {
-	char cwd[PATH_MAX];
-	const char *slash;
-
-	if (0 <= is_bare_repository_cfg)
-		return;
-	if (!git_dir)
-		return;
-
-	/*
-	 * "GIT_DIR=. git init" is always bare.
-	 * "GIT_DIR=`pwd` git init" too.
-	 */
-	if (!strcmp(".", git_dir))
-		goto force_bare;
-	if (!getcwd(cwd, sizeof(cwd)))
-		die("cannot tell cwd");
-	if (!strcmp(git_dir, cwd))
-		goto force_bare;
-	/*
-	 * "GIT_DIR=.git or GIT_DIR=something/.git is usually not.
-	 */
-	if (!strcmp(git_dir, ".git"))
-		return;
-	slash = strrchr(git_dir, '/');
-	if (slash && !strcmp(slash, "/.git"))
-		return;
-
-	/*
-	 * Otherwise it is often bare.  At this point
-	 * we are just guessing.
-	 */
- force_bare:
-	is_bare_repository_cfg = 1;
-	return;
-}
-
-static const char init_db_usage[] =
-"git-init [-q | --quiet] [--template=<template-directory>] [--shared]";
-
-/*
- * If you want to, you can share the DB area with any number of branches.
- * That has advantages: you can save space by sharing all the SHA1 objects.
- * On the other hand, it might just make lookup slower and messier. You
- * be the judge.  The default case is to have one DB per managed directory.
- */
-int cmd_init_db(int argc, const char **argv, const char *prefix)
-{
-	const char *git_dir;
 	const char *sha1_dir;
-	const char *template_dir = NULL;
 	char *path;
-	int len, i, reinit;
-	int quiet = 0;
+	int len, reinit;
 
-	for (i = 1; i < argc; i++, argv++) {
-		const char *arg = argv[1];
-		if (!prefixcmp(arg, "--template="))
-			template_dir = arg+11;
-		else if (!strcmp(arg, "--shared"))
-			shared_repository = PERM_GROUP;
-		else if (!prefixcmp(arg, "--shared="))
-			shared_repository = git_config_perm("arg", arg+9);
-		else if (!strcmp(arg, "-q") || !strcmp(arg, "--quiet"))
-		        quiet = 1;
-		else
-			usage(init_db_usage);
-	}
-
-	/*
-	 * GIT_WORK_TREE makes sense only in conjunction with GIT_DIR
-	 * without --bare.  Catch the error early.
-	 */
-	git_dir = getenv(GIT_DIR_ENVIRONMENT);
-	if ((!git_dir || is_bare_repository_cfg == 1)
-	    && getenv(GIT_WORK_TREE_ENVIRONMENT))
-		die("%s (or --work-tree=<directory>) not allowed without "
-		    "specifying %s (or --git-dir=<directory>)",
-		    GIT_WORK_TREE_ENVIRONMENT,
-		    GIT_DIR_ENVIRONMENT);
-
-	guess_repository_type(git_dir);
-
-	if (is_bare_repository_cfg <= 0) {
-		git_work_tree_cfg = xcalloc(PATH_MAX, 1);
-		if (!getcwd(git_work_tree_cfg, PATH_MAX))
-			die ("Cannot access current working directory.");
-		if (access(get_git_work_tree(), X_OK))
-			die ("Cannot access work tree '%s'",
-			     get_git_work_tree());
-	}
-
-	/*
-	 * Set up the default .git directory contents
-	 */
-	git_dir = getenv(GIT_DIR_ENVIRONMENT);
-	if (!git_dir)
-		git_dir = DEFAULT_GIT_DIR_ENVIRONMENT;
-	safe_create_dir(git_dir, 0);
+	safe_create_dir(get_git_dir(), 0);
 
 	/* Check to see if the repository version is right.
 	 * Note that a newly created repository does not have
@@ -386,11 +292,8 @@ int cmd_init_db(int argc, const char **argv, const char *prefix)
 	 */
 	check_repository_format();
 
-	reinit = create_default_files(git_dir, template_dir);
+	reinit = create_default_files(template_dir);
 
-	/*
-	 * And set up the object store.
-	 */
 	sha1_dir = get_object_directory();
 	len = strlen(sha1_dir);
 	path = xmalloc(len + 40);
@@ -420,11 +323,117 @@ int cmd_init_db(int argc, const char **argv, const char *prefix)
 		git_config_set("receive.denyNonFastforwards", "true");
 	}
 
-	if (!quiet)
+	if (!(flags & INIT_DB_QUIET))
 		printf("%s%s Git repository in %s/\n",
 		       reinit ? "Reinitialized existing" : "Initialized empty",
 		       shared_repository ? " shared" : "",
-		       git_dir);
+		       get_git_dir());
 
 	return 0;
 }
+
+static int guess_repository_type(const char *git_dir)
+{
+	char cwd[PATH_MAX];
+	const char *slash;
+
+	/*
+	 * "GIT_DIR=. git init" is always bare.
+	 * "GIT_DIR=`pwd` git init" too.
+	 */
+	if (!strcmp(".", git_dir))
+		return 1;
+	if (!getcwd(cwd, sizeof(cwd)))
+		die("cannot tell cwd");
+	if (!strcmp(git_dir, cwd))
+		return 1;
+	/*
+	 * "GIT_DIR=.git or GIT_DIR=something/.git is usually not.
+	 */
+	if (!strcmp(git_dir, ".git"))
+		return 0;
+	slash = strrchr(git_dir, '/');
+	if (slash && !strcmp(slash, "/.git"))
+		return 0;
+
+	/*
+	 * Otherwise it is often bare.  At this point
+	 * we are just guessing.
+	 */
+	return 1;
+}
+
+static const char init_db_usage[] =
+"git-init [-q | --quiet] [--template=<template-directory>] [--shared]";
+
+/*
+ * If you want to, you can share the DB area with any number of branches.
+ * That has advantages: you can save space by sharing all the SHA1 objects.
+ * On the other hand, it might just make lookup slower and messier. You
+ * be the judge.  The default case is to have one DB per managed directory.
+ */
+int cmd_init_db(int argc, const char **argv, const char *prefix)
+{
+	const char *git_dir;
+	const char *template_dir = NULL;
+	unsigned int flags = 0;
+	int i;
+
+	for (i = 1; i < argc; i++, argv++) {
+		const char *arg = argv[1];
+		if (!prefixcmp(arg, "--template="))
+			template_dir = arg+11;
+		else if (!strcmp(arg, "--shared"))
+			shared_repository = PERM_GROUP;
+		else if (!prefixcmp(arg, "--shared="))
+			shared_repository = git_config_perm("arg", arg+9);
+		else if (!strcmp(arg, "-q") || !strcmp(arg, "--quiet"))
+			flags |= INIT_DB_QUIET;
+		else
+			usage(init_db_usage);
+	}
+
+	/*
+	 * GIT_WORK_TREE makes sense only in conjunction with GIT_DIR
+	 * without --bare.  Catch the error early.
+	 */
+	git_dir = getenv(GIT_DIR_ENVIRONMENT);
+	if ((!git_dir || is_bare_repository_cfg == 1)
+	    && getenv(GIT_WORK_TREE_ENVIRONMENT))
+		die("%s (or --work-tree=<directory>) not allowed without "
+		    "specifying %s (or --git-dir=<directory>)",
+		    GIT_WORK_TREE_ENVIRONMENT,
+		    GIT_DIR_ENVIRONMENT);
+
+	/*
+	 * Set up the default .git directory contents
+	 */
+	if (!git_dir)
+		git_dir = DEFAULT_GIT_DIR_ENVIRONMENT;
+
+	if (is_bare_repository_cfg < 0)
+		is_bare_repository_cfg = guess_repository_type(git_dir);
+
+	if (!is_bare_repository_cfg) {
+		if (git_dir) {
+			const char *git_dir_parent = strrchr(git_dir, '/');
+			if (git_dir_parent) {
+				char *rel = xstrndup(git_dir, git_dir_parent - git_dir);
+				git_work_tree_cfg = xstrdup(make_absolute_path(rel));
+				free(rel);
+			}
+		}
+		if (!git_work_tree_cfg) {
+			git_work_tree_cfg = xcalloc(PATH_MAX, 1);
+			if (!getcwd(git_work_tree_cfg, PATH_MAX))
+				die ("Cannot access current working directory.");
+		}
+		if (access(get_git_work_tree(), X_OK))
+			die ("Cannot access work tree '%s'",
+			     get_git_work_tree());
+	}
+
+	set_git_dir(make_absolute_path(git_dir));
+
+	return init_db(template_dir, flags);
+}
diff --git a/builtin.h b/builtin.h
index 95126fd0c1..23a90ded7d 100644
--- a/builtin.h
+++ b/builtin.h
@@ -24,6 +24,7 @@ extern int cmd_check_attr(int argc, const char **argv, const char *prefix);
 extern int cmd_check_ref_format(int argc, const char **argv, const char *prefix);
 extern int cmd_cherry(int argc, const char **argv, const char *prefix);
 extern int cmd_cherry_pick(int argc, const char **argv, const char *prefix);
+extern int cmd_clone(int argc, const char **argv, const char *prefix);
 extern int cmd_clean(int argc, const char **argv, const char *prefix);
 extern int cmd_commit(int argc, const char **argv, const char *prefix);
 extern int cmd_commit_tree(int argc, const char **argv, const char *prefix);
diff --git a/cache.h b/cache.h
index ef330b4c6b..3d4e8e77d8 100644
--- a/cache.h
+++ b/cache.h
@@ -317,6 +317,7 @@ extern char *get_graft_file(void);
 extern int set_git_dir(const char *path);
 extern const char *get_git_work_tree(void);
 extern const char *read_gitfile_gently(const char *path);
+extern void set_git_work_tree(const char *tree);
 
 #define ALTERNATE_DB_ENVIRONMENT "GIT_ALTERNATE_OBJECT_DIRECTORIES"
 
@@ -329,6 +330,10 @@ extern const char *prefix_filename(const char *prefix, int len, const char *path
 extern void verify_filename(const char *prefix, const char *name);
 extern void verify_non_filename(const char *prefix, const char *name);
 
+#define INIT_DB_QUIET 0x0001
+
+extern int init_db(const char *template_dir, unsigned int flags);
+
 #define alloc_nr(x) (((x)+16)*3/2)
 
 /*
@@ -399,6 +404,7 @@ struct lock_file {
 	char filename[PATH_MAX];
 };
 extern int hold_lock_file_for_update(struct lock_file *, const char *path, int);
+extern int hold_lock_file_for_append(struct lock_file *, const char *path, int);
 extern int commit_lock_file(struct lock_file *);
 
 extern int hold_locked_index(struct lock_file *, int);
@@ -616,6 +622,7 @@ extern struct alternate_object_database {
 	char base[FLEX_ARRAY]; /* more */
 } *alt_odb_list;
 extern void prepare_alt_odb(void);
+extern void add_to_alternates_file(const char *reference);
 
 struct pack_window {
 	struct pack_window *next;
diff --git a/git-clone.sh b/contrib/examples/git-clone.sh
similarity index 100%
rename from git-clone.sh
rename to contrib/examples/git-clone.sh
diff --git a/environment.c b/environment.c
index 4fcb471248..73feb2d03a 100644
--- a/environment.c
+++ b/environment.c
@@ -44,7 +44,7 @@ enum rebase_setup_type autorebase = AUTOREBASE_NEVER;
 
 /* This is set by setup_git_dir_gently() and/or git_default_config() */
 char *git_work_tree_cfg;
-static const char *work_tree;
+static char *work_tree;
 
 static const char *git_dir;
 static char *git_object_dir, *git_index_file, *git_refs_dir, *git_graft_file;
@@ -86,10 +86,26 @@ const char *get_git_dir(void)
 	return git_dir;
 }
 
+static int git_work_tree_initialized;
+
+/*
+ * Note.  This works only before you used a work tree.  This was added
+ * primarily to support git-clone to work in a new repository it just
+ * created, and is not meant to flip between different work trees.
+ */
+void set_git_work_tree(const char *new_work_tree)
+{
+	if (is_bare_repository_cfg >= 0)
+		die("cannot set work tree after initialization");
+	git_work_tree_initialized = 1;
+	free(work_tree);
+	work_tree = xstrdup(make_absolute_path(new_work_tree));
+	is_bare_repository_cfg = 0;
+}
+
 const char *get_git_work_tree(void)
 {
-	static int initialized = 0;
-	if (!initialized) {
+	if (!git_work_tree_initialized) {
 		work_tree = getenv(GIT_WORK_TREE_ENVIRONMENT);
 		/* core.bare = true overrides implicit and config work tree */
 		if (!work_tree && is_bare_repository_cfg < 1) {
@@ -99,7 +115,7 @@ const char *get_git_work_tree(void)
 				work_tree = xstrdup(make_absolute_path(git_path(work_tree)));
 		} else if (work_tree)
 			work_tree = xstrdup(make_absolute_path(work_tree));
-		initialized = 1;
+		git_work_tree_initialized = 1;
 		if (work_tree)
 			is_bare_repository_cfg = 0;
 	}
diff --git a/git.c b/git.c
index 89b431fa28..2c9004f02e 100644
--- a/git.c
+++ b/git.c
@@ -286,6 +286,7 @@ static void handle_internal_command(int argc, const char **argv)
 		{ "check-attr", cmd_check_attr, RUN_SETUP | NEED_WORK_TREE },
 		{ "cherry", cmd_cherry, RUN_SETUP },
 		{ "cherry-pick", cmd_cherry_pick, RUN_SETUP | NEED_WORK_TREE },
+		{ "clone", cmd_clone },
 		{ "clean", cmd_clean, RUN_SETUP | NEED_WORK_TREE },
 		{ "commit", cmd_commit, RUN_SETUP | NEED_WORK_TREE },
 		{ "commit-tree", cmd_commit_tree, RUN_SETUP },
diff --git a/lockfile.c b/lockfile.c
index b0118d0592..cfc7335347 100644
--- a/lockfile.c
+++ b/lockfile.c
@@ -160,6 +160,34 @@ int hold_lock_file_for_update(struct lock_file *lk, const char *path, int die_on
 	return fd;
 }
 
+int hold_lock_file_for_append(struct lock_file *lk, const char *path, int die_on_error)
+{
+	int fd, orig_fd;
+
+	fd = lock_file(lk, path);
+	if (fd < 0) {
+		if (die_on_error)
+			die("unable to create '%s.lock': %s", path, strerror(errno));
+		return fd;
+	}
+
+	orig_fd = open(path, O_RDONLY);
+	if (orig_fd < 0) {
+		if (errno != ENOENT) {
+			if (die_on_error)
+				die("cannot open '%s' for copying", path);
+			close(fd);
+			return error("cannot open '%s' for copying", path);
+		}
+	} else if (copy_fd(orig_fd, fd)) {
+		if (die_on_error)
+			exit(128);
+		close(fd);
+		return -1;
+	}
+	return fd;
+}
+
 int close_lock_file(struct lock_file *lk)
 {
 	int fd = lk->fd;
diff --git a/refs.c b/refs.c
index 9b495eb16e..9e8e8581ba 100644
--- a/refs.c
+++ b/refs.c
@@ -159,6 +159,8 @@ static struct cached_refs {
 } cached_refs;
 static struct ref_list *current_ref;
 
+static struct ref_list *extra_refs;
+
 static void free_ref_list(struct ref_list *list)
 {
 	struct ref_list *next;
@@ -215,6 +217,17 @@ static void read_packed_refs(FILE *f, struct cached_refs *cached_refs)
 	cached_refs->packed = sort_ref_list(list);
 }
 
+void add_extra_ref(const char *name, const unsigned char *sha1, int flag)
+{
+	extra_refs = add_ref(name, sha1, flag, extra_refs, NULL);
+}
+
+void clear_extra_refs(void)
+{
+	free_ref_list(extra_refs);
+	extra_refs = NULL;
+}
+
 static struct ref_list *get_packed_refs(void)
 {
 	if (!cached_refs.did_packed) {
@@ -547,6 +560,11 @@ static int do_for_each_ref(const char *base, each_ref_fn fn, int trim,
 	struct ref_list *packed = get_packed_refs();
 	struct ref_list *loose = get_loose_refs();
 
+	struct ref_list *extra;
+
+	for (extra = extra_refs; extra; extra = extra->next)
+		retval = do_one_ref(base, fn, trim, cb_data, extra);
+
 	while (packed && loose) {
 		struct ref_list *entry;
 		int cmp = strcmp(packed->name, loose->name);
diff --git a/refs.h b/refs.h
index 06abee1526..06ad260556 100644
--- a/refs.h
+++ b/refs.h
@@ -24,6 +24,15 @@ extern int for_each_tag_ref(each_ref_fn, void *);
 extern int for_each_branch_ref(each_ref_fn, void *);
 extern int for_each_remote_ref(each_ref_fn, void *);
 
+/*
+ * Extra refs will be listed by for_each_ref() before any actual refs
+ * for the duration of this process or until clear_extra_refs() is
+ * called. Only extra refs added before for_each_ref() is called will
+ * be listed on a given call of for_each_ref().
+ */
+extern void add_extra_ref(const char *refname, const unsigned char *sha1, int flags);
+extern void clear_extra_refs(void);
+
 extern int peel_ref(const char *, unsigned char *);
 
 /** Locks a "refs/" ref returning the lock on success and NULL on failure. **/
diff --git a/remote.c b/remote.c
index 9e4f2b84d9..75a12c0762 100644
--- a/remote.c
+++ b/remote.c
@@ -2,6 +2,16 @@
 #include "remote.h"
 #include "refs.h"
 
+static struct refspec s_tag_refspec = {
+	0,
+	1,
+	0,
+	"refs/tags/",
+	"refs/tags/"
+};
+
+const struct refspec *tag_refspec = &s_tag_refspec;
+
 struct counted_string {
 	size_t len;
 	const char *s;
diff --git a/remote.h b/remote.h
index c2f557357f..8eed87ba5a 100644
--- a/remote.h
+++ b/remote.h
@@ -53,6 +53,8 @@ struct refspec {
 	char *dst;
 };
 
+extern const struct refspec *tag_refspec;
+
 struct ref *alloc_ref(unsigned namelen);
 
 struct ref *alloc_ref_from_str(const char* str);
diff --git a/sha1_file.c b/sha1_file.c
index c3170961ce..9679040d62 100644
--- a/sha1_file.c
+++ b/sha1_file.c
@@ -370,6 +370,18 @@ static void read_info_alternates(const char * relative_base, int depth)
 	munmap(map, mapsz);
 }
 
+void add_to_alternates_file(const char *reference)
+{
+	struct lock_file *lock = xcalloc(1, sizeof(struct lock_file));
+	int fd = hold_lock_file_for_append(lock, git_path("objects/info/alternates"), 1);
+	char *alt = mkpath("%s/objects\n", reference);
+	write_or_die(fd, alt, strlen(alt));
+	if (commit_lock_file(lock))
+		die("could not close alternates file");
+	if (alt_odb_tail)
+		link_alt_odb_entries(alt, alt + strlen(alt), '\n', NULL, 0);
+}
+
 void prepare_alt_odb(void)
 {
 	const char *alt;
diff --git a/t/t5601-clone.sh b/t/t5601-clone.sh
index dc9d63dbf9..593d1a3877 100755
--- a/t/t5601-clone.sh
+++ b/t/t5601-clone.sh
@@ -23,4 +23,11 @@ test_expect_success 'clone with excess parameters' '
 
 '
 
+test_expect_success 'clone checks out files' '
+
+	git clone src dst &&
+	test -f dst/file
+
+'
+
 test_done
diff --git a/t/t5700-clone-reference.sh b/t/t5700-clone-reference.sh
index e5619a9f5c..e1ca7303ac 100755
--- a/t/t5700-clone-reference.sh
+++ b/t/t5700-clone-reference.sh
@@ -8,6 +8,8 @@ test_description='test clone --reference'
 
 base_dir=`pwd`
 
+U=$base_dir/UPLOAD_LOG
+
 test_expect_success 'preparing first repository' \
 'test_create_repo A && cd A &&
 echo first > file1 &&
@@ -50,8 +52,13 @@ diff expected current'
 
 cd "$base_dir"
 
+rm -f $U
+
 test_expect_success 'cloning with reference (no -l -s)' \
-'git clone --reference B "file://$(pwd)/A" D'
+'GIT_DEBUG_SEND_PACK=3 git clone --reference B "file://$(pwd)/A" D 3>$U'
+
+test_expect_success 'fetched no objects' \
+'! grep "^want" $U'
 
 cd "$base_dir"
 
@@ -113,4 +120,30 @@ diff expected current'
 
 cd "$base_dir"
 
+test_expect_success 'preparing alternate repository #1' \
+'test_create_repo F && cd F &&
+echo first > file1 &&
+git add file1 &&
+git commit -m initial'
+
+cd "$base_dir"
+
+test_expect_success 'cloning alternate repo #2 and adding changes to repo #1' \
+'git clone F G && cd F &&
+echo second > file2 &&
+git add file2 &&
+git commit -m addition'
+
+cd "$base_dir"
+
+test_expect_success 'cloning alternate repo #1, using #2 as reference' \
+'git clone --reference G F H'
+
+cd "$base_dir"
+
+test_expect_success 'cloning with reference being subset of source (-l -s)' \
+'git clone -l -s --reference A B E'
+
+cd "$base_dir"
+
 test_done
diff --git a/transport.c b/transport.c
index 1bc16f2b65..3ff851935f 100644
--- a/transport.c
+++ b/transport.c
@@ -203,7 +203,7 @@ static struct ref *get_refs_via_rsync(struct transport *transport)
 }
 
 static int fetch_objs_via_rsync(struct transport *transport,
-				 int nr_objs, struct ref **to_fetch)
+				int nr_objs, const struct ref **to_fetch)
 {
 	struct strbuf buf = STRBUF_INIT;
 	struct child_process rsync;
@@ -350,7 +350,7 @@ static int rsync_transport_push(struct transport *transport,
 
 #ifndef NO_CURL /* http fetch is the only user */
 static int fetch_objs_via_walker(struct transport *transport,
-				 int nr_objs, struct ref **to_fetch)
+				 int nr_objs, const struct ref **to_fetch)
 {
 	char *dest = xstrdup(transport->url);
 	struct walker *walker = transport->data;
@@ -517,7 +517,7 @@ static struct ref *get_refs_via_curl(struct transport *transport)
 }
 
 static int fetch_objs_via_curl(struct transport *transport,
-				 int nr_objs, struct ref **to_fetch)
+				 int nr_objs, const struct ref **to_fetch)
 {
 	if (!transport->data)
 		transport->data = get_http_walker(transport->url,
@@ -554,7 +554,7 @@ static struct ref *get_refs_from_bundle(struct transport *transport)
 }
 
 static int fetch_refs_from_bundle(struct transport *transport,
-			       int nr_heads, struct ref **to_fetch)
+			       int nr_heads, const struct ref **to_fetch)
 {
 	struct bundle_transport_data *data = transport->data;
 	return unbundle(&data->header, data->fd);
@@ -628,7 +628,7 @@ static struct ref *get_refs_via_connect(struct transport *transport)
 }
 
 static int fetch_refs_via_pack(struct transport *transport,
-			       int nr_heads, struct ref **to_fetch)
+			       int nr_heads, const struct ref **to_fetch)
 {
 	struct git_transport_data *data = transport->data;
 	char **heads = xmalloc(nr_heads * sizeof(*heads));
@@ -796,12 +796,12 @@ const struct ref *transport_get_remote_refs(struct transport *transport)
 	return transport->remote_refs;
 }
 
-int transport_fetch_refs(struct transport *transport, struct ref *refs)
+int transport_fetch_refs(struct transport *transport, const struct ref *refs)
 {
 	int rc;
 	int nr_heads = 0, nr_alloc = 0;
-	struct ref **heads = NULL;
-	struct ref *rm;
+	const struct ref **heads = NULL;
+	const struct ref *rm;
 
 	for (rm = refs; rm; rm = rm->next) {
 		if (rm->peer_ref &&
diff --git a/transport.h b/transport.h
index 8abfc0ae60..d0b52053ff 100644
--- a/transport.h
+++ b/transport.h
@@ -19,7 +19,7 @@ struct transport {
 			  const char *value);
 
 	struct ref *(*get_refs_list)(struct transport *transport);
-	int (*fetch)(struct transport *transport, int refs_nr, struct ref **refs);
+	int (*fetch)(struct transport *transport, int refs_nr, const struct ref **refs);
 	int (*push)(struct transport *connection, int refspec_nr, const char **refspec, int flags);
 
 	int (*disconnect)(struct transport *connection);
@@ -68,7 +68,7 @@ int transport_push(struct transport *connection,
 
 const struct ref *transport_get_remote_refs(struct transport *transport);
 
-int transport_fetch_refs(struct transport *transport, struct ref *refs);
+int transport_fetch_refs(struct transport *transport, const struct ref *refs);
 void transport_unlock_pack(struct transport *transport);
 int transport_disconnect(struct transport *transport);