From: Junio C Hamano <junkio@cox.net>
Date: Sat, 20 May 2006 00:02:22 +0000 (-0700)
Subject: Merge branch 'jc/read-tree-safety'
X-Git-Tag: v1.4.0-rc1~114
X-Git-Url: https://www.git.lorimer.id.au/gitweb.git/diff_plain/0081e36c9dc3c201e22f12ebebadfff88fa32b91?hp=fcc387db9bc453dc7e07a262873481af2ee9e5c8

Merge branch 'jc/read-tree-safety'

* jc/read-tree-safety:
read-tree -m -u: do not overwrite or remove untracked working tree files.
---

diff --git a/Documentation/SubmittingPatches b/Documentation/SubmittingPatches
index 318b04fdeb..8601949e80 100644
--- a/Documentation/SubmittingPatches
+++ b/Documentation/SubmittingPatches
@@ -266,8 +266,8 @@ This recipe appears to work with the current [*1*] Thunderbird from Suse.
 The following Thunderbird extensions are needed:
 	AboutConfig 0.5
 		http://aboutconfig.mozdev.org/
-	External Editor 0.5.4
-		http://extensionroom.mozdev.org/more-info/exteditor
+	External Editor 0.7.2
+		http://globs.org/articles.php?lng=en&pg=8
 
 1) Prepare the patch as a text file using your method of choice.
 
diff --git a/Documentation/git-quiltimport.txt b/Documentation/git-quiltimport.txt
new file mode 100644
index 0000000000..6e9a8c369a
--- /dev/null
+++ b/Documentation/git-quiltimport.txt
@@ -0,0 +1,61 @@
+git-quiltimport(1)
+================
+
+NAME
+----
+git-quiltimport - Applies a quilt patchset onto the current branch
+
+
+SYNOPSIS
+--------
+[verse]
+'git-quiltimport' [--dry-run] [--author <author>] [--patches <dir>]
+
+
+DESCRIPTION
+-----------
+Applies a quilt patchset onto the current git branch, preserving
+the patch boundaries, patch order, and patch descriptions present
+in the quilt patchset.
+
+For each patch the code attempts to extract the author from the
+patch description.  If that fails it falls back to the author
+specified with --author.  If the --author flag was not given
+the patch description is displayed and the user is asked to
+interactively enter the author of the patch.
+
+If a subject is not found in the patch description the patch name is
+preserved as the 1 line subject in the git description.
+
+OPTIONS
+-------
+--dry-run::
+	Walk through the patches in the series and warn
+	if we cannot find all of the necessary information to commit
+	a patch.  At the time of this writing only missing author
+	information is warned about.
+
+--author Author Name <Author Email>::
+	The author name and email address to use when no author
+	information can be found in the patch description.
+
+--patches <dir>::
+	The directory to find the quilt patches and the
+	quilt series file.
+
+        The default for the patch directory is patches
+	or the value of the $QUILT_PATCHES environment
+	variable.
+
+Author
+------
+Written by Eric Biederman <ebiederm@lnxi.com>
+
+Documentation
+--------------
+Documentation by Eric Biederman <ebiederm@lnxi.com>
+
+GIT
+---
+Part of the gitlink:git[7] suite
+
diff --git a/Documentation/install-webdoc.sh b/Documentation/install-webdoc.sh
index 50638c78d5..60211a5058 100755
--- a/Documentation/install-webdoc.sh
+++ b/Documentation/install-webdoc.sh
@@ -4,12 +4,16 @@ T="$1"
 
 for h in *.html *.txt howto/*.txt howto/*.html
 do
-	diff -u -I'Last updated [0-9][0-9]-[A-Z][a-z][a-z]-' "$T/$h" "$h" || {
+	if test -f "$T/$h" &&
+	   diff -u -I'Last updated [0-9][0-9]-[A-Z][a-z][a-z]-' "$T/$h" "$h"
+	then
+		:; # up to date
+	else
 		echo >&2 "# install $h $T/$h"
 		rm -f "$T/$h"
 		mkdir -p `dirname "$T/$h"`
 		cp "$h" "$T/$h"
-	}
+	fi
 done
 strip_leading=`echo "$T/" | sed -e 's|.|.|g'`
 for th in "$T"/*.html "$T"/*.txt "$T"/howto/*.txt "$T"/howto/*.html
diff --git a/Makefile b/Makefile
index 9ba608c805..3a31ce0150 100644
--- a/Makefile
+++ b/Makefile
@@ -125,7 +125,7 @@ SCRIPT_SH = \
 	git-applymbox.sh git-applypatch.sh git-am.sh \
 	git-merge.sh git-merge-stupid.sh git-merge-octopus.sh \
 	git-merge-resolve.sh git-merge-ours.sh \
-	git-lost-found.sh
+	git-lost-found.sh git-quiltimport.sh
 
 SCRIPT_PERL = \
 	git-archimport.perl git-cvsimport.perl git-relink.perl \
@@ -154,23 +154,24 @@ PROGRAMS = \
 	git-convert-objects$X git-diff-files$X \
 	git-diff-index$X git-diff-stages$X \
 	git-diff-tree$X git-fetch-pack$X git-fsck-objects$X \
-	git-hash-object$X git-index-pack$X git-init-db$X git-local-fetch$X \
+	git-hash-object$X git-index-pack$X git-local-fetch$X \
 	git-ls-files$X git-ls-tree$X git-mailinfo$X git-merge-base$X \
 	git-merge-index$X git-mktag$X git-mktree$X git-pack-objects$X git-patch-id$X \
 	git-peek-remote$X git-prune-packed$X git-read-tree$X \
-	git-receive-pack$X git-rev-list$X git-rev-parse$X \
+	git-receive-pack$X git-rev-parse$X \
 	git-send-pack$X git-show-branch$X git-shell$X \
 	git-show-index$X git-ssh-fetch$X \
 	git-ssh-upload$X git-tar-tree$X git-unpack-file$X \
 	git-unpack-objects$X git-update-index$X git-update-server-info$X \
 	git-upload-pack$X git-verify-pack$X git-write-tree$X \
-	git-update-ref$X git-symbolic-ref$X git-check-ref-format$X \
+	git-update-ref$X git-symbolic-ref$X \
 	git-name-rev$X git-pack-redundant$X git-repo-config$X git-var$X \
 	git-describe$X git-merge-tree$X git-blame$X git-imap-send$X
 
 BUILT_INS = git-log$X git-whatchanged$X git-show$X \
 	git-count-objects$X git-diff$X git-push$X \
-	git-grep$X
+	git-grep$X git-rev-list$X git-check-ref-format$X \
+	git-init-db$X
 
 # what 'all' will build and 'install' will install, in gitexecdir
 ALL_PROGRAMS = $(PROGRAMS) $(SIMPLE_PROGRAMS) $(SCRIPTS)
@@ -218,7 +219,8 @@ LIB_OBJS = \
 
 BUILTIN_OBJS = \
 	builtin-log.o builtin-help.o builtin-count.o builtin-diff.o builtin-push.o \
-	builtin-grep.o
+	builtin-grep.o builtin-rev-list.o builtin-check-ref-format.o \
+	builtin-init-db.o
 
 GITLIBS = $(LIB_FILE) $(XDIFF_LIB)
 LIBS = $(GITLIBS) -lz
@@ -473,6 +475,7 @@ strip: $(PROGRAMS) git$X
 
 git$X: git.c common-cmds.h $(BUILTIN_OBJS) $(GITLIBS)
 	$(CC) -DGIT_VERSION='"$(GIT_VERSION)"' \
+		-DDEFAULT_GIT_TEMPLATE_DIR='"$(template_dir_SQ)"' \
 		$(ALL_CFLAGS) -o $@ $(filter %.c,$^) \
 		$(BUILTIN_OBJS) $(ALL_LDFLAGS) $(LIBS)
 
@@ -565,10 +568,6 @@ git-http-push$X: revision.o http.o http-push.o $(LIB_FILE)
 	$(CC) $(ALL_CFLAGS) -o $@ $(ALL_LDFLAGS) $(filter %.o,$^) \
 		$(LIBS) $(CURL_LIBCURL) $(EXPAT_LIBEXPAT)
 
-init-db.o: init-db.c
-	$(CC) -c $(ALL_CFLAGS) \
-		-DDEFAULT_GIT_TEMPLATE_DIR='"$(template_dir_SQ)"' $*.c
-
 $(LIB_OBJS) $(BUILTIN_OBJS): $(LIB_H)
 $(patsubst git-%$X,%.o,$(PROGRAMS)): $(GITLIBS)
 $(DIFF_OBJS): diffcore.h
@@ -652,6 +651,25 @@ dist: git.spec git-tar-tree
 rpm: dist
 	$(RPMBUILD) -ta $(GIT_TARNAME).tar.gz
 
+htmldocs = git-htmldocs-$(GIT_VERSION)
+manpages = git-manpages-$(GIT_VERSION)
+dist-doc:
+	rm -fr .doc-tmp-dir
+	mkdir .doc-tmp-dir
+	$(MAKE) -C Documentation WEBDOC_DEST=../.doc-tmp-dir install-webdoc
+	cd .doc-tmp-dir && $(TAR) cf ../$(htmldocs).tar .
+	gzip -n -9 -f $(htmldocs).tar
+	:
+	rm -fr .doc-tmp-dir
+	mkdir .doc-tmp-dir .doc-tmp-dir/man1 .doc-tmp-dir/man7
+	$(MAKE) -C Documentation DESTDIR=. \
+		man1=../.doc-tmp-dir/man1 \
+		man7=../.doc-tmp-dir/man7 \
+		install
+	cd .doc-tmp-dir && $(TAR) cf ../$(manpages).tar .
+	gzip -n -9 -f $(manpages).tar
+	rm -fr .doc-tmp-dir
+
 ### Cleaning rules
 
 clean:
@@ -659,8 +677,9 @@ clean:
 		$(LIB_FILE) $(XDIFF_LIB)
 	rm -f $(ALL_PROGRAMS) $(BUILT_INS) git$X
 	rm -f *.spec *.pyc *.pyo */*.pyc */*.pyo common-cmds.h TAGS tags
-	rm -rf $(GIT_TARNAME)
+	rm -rf $(GIT_TARNAME) .doc-tmp-dir
 	rm -f $(GIT_TARNAME).tar.gz git-core_$(GIT_VERSION)-*.tar.gz
+	rm -f $(htmldocs).tar $(manpages).tar
 	$(MAKE) -C Documentation/ clean
 	$(MAKE) -C templates clean
 	$(MAKE) -C t/ clean
diff --git a/apply.c b/apply.c
index 7c8146a7f3..0ed9d132e8 100644
--- a/apply.c
+++ b/apply.c
@@ -17,6 +17,8 @@
 //  --stat does just a diffstat, and doesn't actually apply
 //  --numstat does numeric diffstat, and doesn't actually apply
 //  --index-info shows the old and new index info for paths if available.
+//  --index updates the cache as well.
+//  --cached updates only the cache without ever touching the working tree.
 //
 static const char *prefix;
 static int prefix_length = -1;
@@ -26,6 +28,7 @@ static int p_value = 1;
 static int allow_binary_replacement = 0;
 static int check_index = 0;
 static int write_index = 0;
+static int cached = 0;
 static int diffstat = 0;
 static int numstat = 0;
 static int summary = 0;
@@ -36,7 +39,7 @@ static int show_index_info = 0;
 static int line_termination = '\n';
 static unsigned long p_context = -1;
 static const char apply_usage[] =
-"git-apply [--stat] [--numstat] [--summary] [--check] [--index] [--apply] [--no-add] [--index-info] [--allow-binary-replacement] [-z] [-pNUM] [-CNUM] [--whitespace=<nowarn|warn|error|error-all|strip>] <patch>...";
+"git-apply [--stat] [--numstat] [--summary] [--check] [--index] [--cached] [--apply] [--no-add] [--index-info] [--allow-binary-replacement] [-z] [-pNUM] [-CNUM] [--whitespace=<nowarn|warn|error|error-all|strip>] <patch>...";
 
 static enum whitespace_eol {
 	nowarn_whitespace,
@@ -1600,7 +1603,7 @@ static int apply_fragments(struct buffer_desc *desc, struct patch *patch)
 	return 0;
 }
 
-static int apply_data(struct patch *patch, struct stat *st)
+static int apply_data(struct patch *patch, struct stat *st, struct cache_entry *ce)
 {
 	char *buf;
 	unsigned long size, alloc;
@@ -1609,7 +1612,17 @@ static int apply_data(struct patch *patch, struct stat *st)
 	size = 0;
 	alloc = 0;
 	buf = NULL;
-	if (patch->old_name) {
+	if (cached) {
+		if (ce) {
+			char type[20];
+			buf = read_sha1_file(ce->sha1, type, &size);
+			if (!buf)
+				return error("read of %s failed",
+					     patch->old_name);
+			alloc = size;
+		}
+	}
+	else if (patch->old_name) {
 		size = st->st_size;
 		alloc = size + 8192;
 		buf = xmalloc(alloc);
@@ -1637,16 +1650,21 @@ static int check_patch(struct patch *patch)
 	const char *old_name = patch->old_name;
 	const char *new_name = patch->new_name;
 	const char *name = old_name ? old_name : new_name;
+	struct cache_entry *ce = NULL;
 
 	if (old_name) {
-		int changed;
-		int stat_ret = lstat(old_name, &st);
+		int changed = 0;
+		int stat_ret = 0;
+		unsigned st_mode = 0;
 
+		if (!cached)
+			stat_ret = lstat(old_name, &st);
 		if (check_index) {
 			int pos = cache_name_pos(old_name, strlen(old_name));
 			if (pos < 0)
 				return error("%s: does not exist in index",
 					     old_name);
+			ce = active_cache[pos];
 			if (stat_ret < 0) {
 				struct checkout costate;
 				if (errno != ENOENT)
@@ -1659,40 +1677,46 @@ static int check_patch(struct patch *patch)
 				costate.quiet = 0;
 				costate.not_new = 0;
 				costate.refresh_cache = 1;
-				if (checkout_entry(active_cache[pos],
+				if (checkout_entry(ce,
 						   &costate,
 						   NULL) ||
 				    lstat(old_name, &st))
 					return -1;
 			}
-
-			changed = ce_match_stat(active_cache[pos], &st, 1);
+			if (!cached)
+				changed = ce_match_stat(ce, &st, 1);
 			if (changed)
 				return error("%s: does not match index",
 					     old_name);
+			if (cached)
+				st_mode = ntohl(ce->ce_mode);
 		}
 		else if (stat_ret < 0)
 			return error("%s: %s", old_name, strerror(errno));
 
+		if (!cached)
+			st_mode = ntohl(create_ce_mode(st.st_mode));
+
 		if (patch->is_new < 0)
 			patch->is_new = 0;
-		st.st_mode = ntohl(create_ce_mode(st.st_mode));
 		if (!patch->old_mode)
-			patch->old_mode = st.st_mode;
-		if ((st.st_mode ^ patch->old_mode) & S_IFMT)
+			patch->old_mode = st_mode;
+		if ((st_mode ^ patch->old_mode) & S_IFMT)
 			return error("%s: wrong type", old_name);
-		if (st.st_mode != patch->old_mode)
+		if (st_mode != patch->old_mode)
 			fprintf(stderr, "warning: %s has type %o, expected %o\n",
-				old_name, st.st_mode, patch->old_mode);
+				old_name, st_mode, patch->old_mode);
 	}
 
 	if (new_name && (patch->is_new | patch->is_rename | patch->is_copy)) {
 		if (check_index && cache_name_pos(new_name, strlen(new_name)) >= 0)
 			return error("%s: already exists in index", new_name);
-		if (!lstat(new_name, &st))
-			return error("%s: already exists in working directory", new_name);
-		if (errno != ENOENT)
-			return error("%s: %s", new_name, strerror(errno));
+		if (!cached) {
+			if (!lstat(new_name, &st))
+				return error("%s: already exists in working directory", new_name);
+			if (errno != ENOENT)
+				return error("%s: %s", new_name, strerror(errno));
+		}
 		if (!patch->new_mode) {
 			if (patch->is_new)
 				patch->new_mode = S_IFREG | 0644;
@@ -1709,9 +1733,9 @@ static int check_patch(struct patch *patch)
 			return error("new mode (%o) of %s does not match old mode (%o)%s%s",
 				patch->new_mode, new_name, patch->old_mode,
 				same ? "" : " of ", same ? "" : old_name);
-	}	
+	}
 
-	if (apply_data(patch, &st) < 0)
+	if (apply_data(patch, &st, ce) < 0)
 		return error("%s: patch does not apply", name);
 	return 0;
 }
@@ -1778,7 +1802,7 @@ static void numstat_patch_list(struct patch *patch)
 {
 	for ( ; patch; patch = patch->next) {
 		const char *name;
-		name = patch->old_name ? patch->old_name : patch->new_name;
+		name = patch->new_name ? patch->new_name : patch->old_name;
 		printf("%d\t%d\t", patch->lines_added, patch->lines_deleted);
 		if (line_termination && quote_c_style(name, NULL, NULL, 0))
 			quote_c_style(name, NULL, stdout, 0);
@@ -1894,7 +1918,8 @@ static void remove_file(struct patch *patch)
 		if (remove_file_from_cache(patch->old_name) < 0)
 			die("unable to remove %s from index", patch->old_name);
 	}
-	unlink(patch->old_name);
+	if (!cached)
+		unlink(patch->old_name);
 }
 
 static void add_index_file(const char *path, unsigned mode, void *buf, unsigned long size)
@@ -1911,9 +1936,11 @@ static void add_index_file(const char *path, unsigned mode, void *buf, unsigned
 	memcpy(ce->name, path, namelen);
 	ce->ce_mode = create_ce_mode(mode);
 	ce->ce_flags = htons(namelen);
-	if (lstat(path, &st) < 0)
-		die("unable to stat newly created file %s", path);
-	fill_stat_cache_info(ce, &st);
+	if (!cached) {
+		if (lstat(path, &st) < 0)
+			die("unable to stat newly created file %s", path);
+		fill_stat_cache_info(ce, &st);
+	}
 	if (write_sha1_file(buf, size, blob_type, ce->sha1) < 0)
 		die("unable to create backing store for newly created file %s", path);
 	if (add_cache_entry(ce, ADD_CACHE_OK_TO_ADD) < 0)
@@ -1950,6 +1977,8 @@ static int try_create_file(const char *path, unsigned int mode, const char *buf,
  */
 static void create_one_file(char *path, unsigned mode, const char *buf, unsigned long size)
 {
+	if (cached)
+		return;
 	if (!try_create_file(path, mode, buf, size))
 		return;
 
@@ -2182,6 +2211,11 @@ int main(int argc, char **argv)
 			check_index = 1;
 			continue;
 		}
+		if (!strcmp(arg, "--cached")) {
+			check_index = 1;
+			cached = 1;
+			continue;
+		}
 		if (!strcmp(arg, "--apply")) {
 			apply = 1;
 			continue;
diff --git a/builtin-check-ref-format.c b/builtin-check-ref-format.c
new file mode 100644
index 0000000000..4a23936aff
--- /dev/null
+++ b/builtin-check-ref-format.c
@@ -0,0 +1,14 @@
+/*
+ * GIT - The information manager from hell
+ */
+
+#include "cache.h"
+#include "refs.h"
+#include "builtin.h"
+
+int cmd_check_ref_format(int argc, const char **argv, char **envp)
+{
+	if (argc != 2)
+		usage("git check-ref-format refname");
+	return !!check_ref_format(argv[1]);
+}
diff --git a/builtin-diff.c b/builtin-diff.c
index b0c9cade02..de81b05e32 100644
--- a/builtin-diff.c
+++ b/builtin-diff.c
@@ -122,7 +122,7 @@ static int builtin_diff_b_f(struct rev_info *revs,
 	stuff_change(&revs->diffopt,
 		     canon_mode(st.st_mode), canon_mode(st.st_mode),
 		     blob[0].sha1, null_sha1,
-		     blob[0].name, path);
+		     path, path);
 	diffcore_std(&revs->diffopt);
 	diff_flush(&revs->diffopt);
 	return 0;
diff --git a/builtin-grep.c b/builtin-grep.c
index 66111de514..d09ddf0485 100644
--- a/builtin-grep.c
+++ b/builtin-grep.c
@@ -453,7 +453,6 @@ static int external_grep(struct grep_opt *opt, const char **paths, int cached)
 
 	len = nr = 0;
 	push_arg("grep");
-	push_arg("-H");
 	if (opt->fixed)
 		push_arg("-F");
 	if (opt->linenum)
@@ -503,17 +502,35 @@ static int external_grep(struct grep_opt *opt, const char **paths, int cached)
 		push_arg("-e");
 		push_arg(p->pattern);
 	}
-	push_arg("--");
+
+	/*
+	 * To make sure we get the header printed out when we want it,
+	 * add /dev/null to the paths to grep.  This is unnecessary
+	 * (and wrong) with "-l" or "-L", which always print out the
+	 * name anyway.
+	 *
+	 * GNU grep has "-H", but this is portable.
+	 */
+	if (!opt->name_only && !opt->unmatch_name_only)
+		push_arg("/dev/null");
 
 	hit = 0;
 	argc = nr;
 	for (i = 0; i < active_nr; i++) {
 		struct cache_entry *ce = active_cache[i];
+		const char *name;
 		if (ce_stage(ce) || !S_ISREG(ntohl(ce->ce_mode)))
 			continue;
 		if (!pathspec_matches(paths, ce->name))
 			continue;
-		argv[argc++] = ce->name;
+		name = ce->name;
+		if (name[0] == '-') {
+			int len = ce_namelen(ce);
+			name = xmalloc(len + 3);
+			memcpy(name, "./", 2);
+			memcpy(name + 2, ce->name, len + 1);
+		}
+		argv[argc++] = name;
 		if (argc < MAXARGS)
 			continue;
 		hit += exec_grep(argc, argv);
diff --git a/builtin-init-db.c b/builtin-init-db.c
new file mode 100644
index 0000000000..2a1384ccb0
--- /dev/null
+++ b/builtin-init-db.c
@@ -0,0 +1,293 @@
+/*
+ * GIT - The information manager from hell
+ *
+ * Copyright (C) Linus Torvalds, 2005
+ */
+#include "cache.h"
+#include "builtin.h"
+
+#ifndef DEFAULT_GIT_TEMPLATE_DIR
+#define DEFAULT_GIT_TEMPLATE_DIR "/usr/share/git-core/templates/"
+#endif
+
+static void safe_create_dir(const char *dir, int share)
+{
+	if (mkdir(dir, 0777) < 0) {
+		if (errno != EEXIST) {
+			perror(dir);
+			exit(1);
+		}
+	}
+	else if (share && adjust_shared_perm(dir))
+		die("Could not make %s writable by group\n", dir);
+}
+
+static int copy_file(const char *dst, const char *src, int mode)
+{
+	int fdi, fdo, status;
+
+	mode = (mode & 0111) ? 0777 : 0666;
+	if ((fdi = open(src, O_RDONLY)) < 0)
+		return fdi;
+	if ((fdo = open(dst, O_WRONLY | O_CREAT | O_EXCL, mode)) < 0) {
+		close(fdi);
+		return fdo;
+	}
+	status = copy_fd(fdi, fdo);
+	close(fdo);
+
+	if (!status && adjust_shared_perm(dst))
+		return -1;
+
+	return status;
+}
+
+static void copy_templates_1(char *path, int baselen,
+			     char *template, int template_baselen,
+			     DIR *dir)
+{
+	struct dirent *de;
+
+	/* Note: if ".git/hooks" file exists in the repository being
+	 * re-initialized, /etc/core-git/templates/hooks/update would
+	 * cause git-init-db to fail here.  I think this is sane but
+	 * it means that the set of templates we ship by default, along
+	 * with the way the namespace under .git/ is organized, should
+	 * be really carefully chosen.
+	 */
+	safe_create_dir(path, 1);
+	while ((de = readdir(dir)) != NULL) {
+		struct stat st_git, st_template;
+		int namelen;
+		int exists = 0;
+
+		if (de->d_name[0] == '.')
+			continue;
+		namelen = strlen(de->d_name);
+		if ((PATH_MAX <= baselen + namelen) ||
+		    (PATH_MAX <= template_baselen + namelen))
+			die("insanely long template name %s", de->d_name);
+		memcpy(path + baselen, de->d_name, namelen+1);
+		memcpy(template + template_baselen, de->d_name, namelen+1);
+		if (lstat(path, &st_git)) {
+			if (errno != ENOENT)
+				die("cannot stat %s", path);
+		}
+		else
+			exists = 1;
+
+		if (lstat(template, &st_template))
+			die("cannot stat template %s", template);
+
+		if (S_ISDIR(st_template.st_mode)) {
+			DIR *subdir = opendir(template);
+			int baselen_sub = baselen + namelen;
+			int template_baselen_sub = template_baselen + namelen;
+			if (!subdir)
+				die("cannot opendir %s", template);
+			path[baselen_sub++] =
+				template[template_baselen_sub++] = '/';
+			path[baselen_sub] =
+				template[template_baselen_sub] = 0;
+			copy_templates_1(path, baselen_sub,
+					 template, template_baselen_sub,
+					 subdir);
+			closedir(subdir);
+		}
+		else if (exists)
+			continue;
+		else if (S_ISLNK(st_template.st_mode)) {
+			char lnk[256];
+			int len;
+			len = readlink(template, lnk, sizeof(lnk));
+			if (len < 0)
+				die("cannot readlink %s", template);
+			if (sizeof(lnk) <= len)
+				die("insanely long symlink %s", template);
+			lnk[len] = 0;
+			if (symlink(lnk, path))
+				die("cannot symlink %s %s", lnk, path);
+		}
+		else if (S_ISREG(st_template.st_mode)) {
+			if (copy_file(path, template, st_template.st_mode))
+				die("cannot copy %s to %s", template, path);
+		}
+		else
+			error("ignoring template %s", template);
+	}
+}
+
+static void copy_templates(const char *git_dir, int len, const char *template_dir)
+{
+	char path[PATH_MAX];
+	char template_path[PATH_MAX];
+	int template_len;
+	DIR *dir;
+
+	if (!template_dir)
+		template_dir = DEFAULT_GIT_TEMPLATE_DIR;
+	strcpy(template_path, template_dir);
+	template_len = strlen(template_path);
+	if (template_path[template_len-1] != '/') {
+		template_path[template_len++] = '/';
+		template_path[template_len] = 0;
+	}
+	dir = opendir(template_path);
+	if (!dir) {
+		fprintf(stderr, "warning: templates not found %s\n",
+			template_dir);
+		return;
+	}
+
+	/* Make sure that template is from the correct vintage */
+	strcpy(template_path + template_len, "config");
+	repository_format_version = 0;
+	git_config_from_file(check_repository_format_version,
+			     template_path);
+	template_path[template_len] = 0;
+
+	if (repository_format_version &&
+	    repository_format_version != GIT_REPO_VERSION) {
+		fprintf(stderr, "warning: not copying templates of "
+			"a wrong format version %d from '%s'\n",
+			repository_format_version,
+			template_dir);
+		closedir(dir);
+		return;
+	}
+
+	memcpy(path, git_dir, len);
+	path[len] = 0;
+	copy_templates_1(path, len,
+			 template_path, template_len,
+			 dir);
+	closedir(dir);
+}
+
+static void create_default_files(const char *git_dir, const char *template_path)
+{
+	unsigned len = strlen(git_dir);
+	static char path[PATH_MAX];
+	unsigned char sha1[20];
+	struct stat st1;
+	char repo_version_string[10];
+
+	if (len > sizeof(path)-50)
+		die("insane git directory %s", git_dir);
+	memcpy(path, git_dir, len);
+
+	if (len && path[len-1] != '/')
+		path[len++] = '/';
+
+	/*
+	 * 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);
+
+	/* 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);
+
+	git_config(git_default_config);
+
+	/*
+	 * Create the default symlink from ".git/HEAD" to the "master"
+	 * branch, if it does not exist yet.
+	 */
+	strcpy(path + len, "HEAD");
+	if (read_ref(path, sha1) < 0) {
+		if (create_symref(path, "refs/heads/master") < 0)
+			exit(1);
+	}
+
+	/* This forces creation of new config file */
+	sprintf(repo_version_string, "%d", GIT_REPO_VERSION);
+	git_config_set("core.repositoryformatversion", repo_version_string);
+
+	path[len] = 0;
+	strcpy(path + len, "config");
+
+	/* Check filemode trustability */
+	if (!lstat(path, &st1)) {
+		struct stat st2;
+		int filemode = (!chmod(path, st1.st_mode ^ S_IXUSR) &&
+				!lstat(path, &st2) &&
+				st1.st_mode != st2.st_mode);
+		git_config_set("core.filemode",
+			       filemode ? "true" : "false");
+	}
+}
+
+static const char init_db_usage[] =
+"git-init-db [--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, char **envp)
+{
+	const char *git_dir;
+	const char *sha1_dir;
+	const char *template_dir = NULL;
+	char *path;
+	int len, i;
+
+	for (i = 1; i < argc; i++, argv++) {
+		const char *arg = argv[1];
+		if (!strncmp(arg, "--template=", 11))
+			template_dir = arg+11;
+		else if (!strcmp(arg, "--shared"))
+			shared_repository = 1;
+		else
+			die(init_db_usage);
+	}
+
+	/*
+	 * Set up the default .git directory contents
+	 */
+	git_dir = getenv(GIT_DIR_ENVIRONMENT);
+	if (!git_dir) {
+		git_dir = DEFAULT_GIT_DIR_ENVIRONMENT;
+		fprintf(stderr, "defaulting to local storage area\n");
+	}
+	safe_create_dir(git_dir, 0);
+
+	/* Check to see if the repository version is right.
+	 * Note that a newly created repository does not have
+	 * config file, so this will not fail.  What we are catching
+	 * is an attempt to reinitialize new repository with an old tool.
+	 */
+	check_repository_format();
+
+	create_default_files(git_dir, template_dir);
+
+	/*
+	 * And set up the object store.
+	 */
+	sha1_dir = get_object_directory();
+	len = strlen(sha1_dir);
+	path = xmalloc(len + 40);
+	memcpy(path, sha1_dir, len);
+
+	safe_create_dir(sha1_dir, 1);
+	strcpy(path+len, "/pack");
+	safe_create_dir(path, 1);
+	strcpy(path+len, "/info");
+	safe_create_dir(path, 1);
+
+	if (shared_repository)
+		git_config_set("core.sharedRepository", "true");
+
+	return 0;
+}
diff --git a/builtin-log.c b/builtin-log.c
index 69f2911cb4..c4ceee0f98 100644
--- a/builtin-log.c
+++ b/builtin-log.c
@@ -19,6 +19,13 @@ static int cmd_log_wc(int argc, const char **argv, char **envp,
 	rev->commit_format = CMIT_FMT_DEFAULT;
 	rev->verbose_header = 1;
 	argc = setup_revisions(argc, argv, rev, "HEAD");
+	if (rev->always_show_header) {
+		if (rev->diffopt.pickaxe || rev->diffopt.filter) {
+			rev->always_show_header = 0;
+			if (rev->diffopt.output_format == DIFF_FORMAT_RAW)
+				rev->diffopt.output_format = DIFF_FORMAT_NO_OUTPUT;
+		}
+	}
 
 	if (argc > 1)
 		die("unrecognized argument: %s", argv[1]);
diff --git a/builtin-rev-list.c b/builtin-rev-list.c
new file mode 100644
index 0000000000..446802d377
--- /dev/null
+++ b/builtin-rev-list.c
@@ -0,0 +1,358 @@
+#include "cache.h"
+#include "refs.h"
+#include "tag.h"
+#include "commit.h"
+#include "tree.h"
+#include "blob.h"
+#include "tree-walk.h"
+#include "diff.h"
+#include "revision.h"
+#include "builtin.h"
+
+/* bits #0-15 in revision.h */
+
+#define COUNTED		(1u<<16)
+
+static const char rev_list_usage[] =
+"git-rev-list [OPTION] <commit-id>... [ -- paths... ]\n"
+"  limiting output:\n"
+"    --max-count=nr\n"
+"    --max-age=epoch\n"
+"    --min-age=epoch\n"
+"    --sparse\n"
+"    --no-merges\n"
+"    --remove-empty\n"
+"    --all\n"
+"  ordering output:\n"
+"    --topo-order\n"
+"    --date-order\n"
+"  formatting output:\n"
+"    --parents\n"
+"    --objects | --objects-edge\n"
+"    --unpacked\n"
+"    --header | --pretty\n"
+"    --abbrev=nr | --no-abbrev\n"
+"    --abbrev-commit\n"
+"  special purpose:\n"
+"    --bisect"
+;
+
+static struct rev_info revs;
+
+static int bisect_list = 0;
+static int show_timestamp = 0;
+static int hdr_termination = 0;
+static const char *header_prefix;
+
+static void show_commit(struct commit *commit)
+{
+	if (show_timestamp)
+		printf("%lu ", commit->date);
+	if (header_prefix)
+		fputs(header_prefix, stdout);
+	if (commit->object.flags & BOUNDARY)
+		putchar('-');
+	if (revs.abbrev_commit && revs.abbrev)
+		fputs(find_unique_abbrev(commit->object.sha1, revs.abbrev),
+		      stdout);
+	else
+		fputs(sha1_to_hex(commit->object.sha1), stdout);
+	if (revs.parents) {
+		struct commit_list *parents = commit->parents;
+		while (parents) {
+			struct object *o = &(parents->item->object);
+			parents = parents->next;
+			if (o->flags & TMP_MARK)
+				continue;
+			printf(" %s", sha1_to_hex(o->sha1));
+			o->flags |= TMP_MARK;
+		}
+		/* TMP_MARK is a general purpose flag that can
+		 * be used locally, but the user should clean
+		 * things up after it is done with them.
+		 */
+		for (parents = commit->parents;
+		     parents;
+		     parents = parents->next)
+			parents->item->object.flags &= ~TMP_MARK;
+	}
+	if (revs.commit_format == CMIT_FMT_ONELINE)
+		putchar(' ');
+	else
+		putchar('\n');
+
+	if (revs.verbose_header) {
+		static char pretty_header[16384];
+		pretty_print_commit(revs.commit_format, commit, ~0,
+				    pretty_header, sizeof(pretty_header),
+				    revs.abbrev);
+		printf("%s%c", pretty_header, hdr_termination);
+	}
+	fflush(stdout);
+}
+
+static struct object_list **process_blob(struct blob *blob,
+					 struct object_list **p,
+					 struct name_path *path,
+					 const char *name)
+{
+	struct object *obj = &blob->object;
+
+	if (!revs.blob_objects)
+		return p;
+	if (obj->flags & (UNINTERESTING | SEEN))
+		return p;
+	obj->flags |= SEEN;
+	return add_object(obj, p, path, name);
+}
+
+static struct object_list **process_tree(struct tree *tree,
+					 struct object_list **p,
+					 struct name_path *path,
+					 const char *name)
+{
+	struct object *obj = &tree->object;
+	struct tree_entry_list *entry;
+	struct name_path me;
+
+	if (!revs.tree_objects)
+		return p;
+	if (obj->flags & (UNINTERESTING | SEEN))
+		return p;
+	if (parse_tree(tree) < 0)
+		die("bad tree object %s", sha1_to_hex(obj->sha1));
+	obj->flags |= SEEN;
+	p = add_object(obj, p, path, name);
+	me.up = path;
+	me.elem = name;
+	me.elem_len = strlen(name);
+	entry = tree->entries;
+	tree->entries = NULL;
+	while (entry) {
+		struct tree_entry_list *next = entry->next;
+		if (entry->directory)
+			p = process_tree(entry->item.tree, p, &me, entry->name);
+		else
+			p = process_blob(entry->item.blob, p, &me, entry->name);
+		free(entry);
+		entry = next;
+	}
+	return p;
+}
+
+static void show_commit_list(struct rev_info *revs)
+{
+	struct commit *commit;
+	struct object_list *objects = NULL, **p = &objects, *pending;
+
+	while ((commit = get_revision(revs)) != NULL) {
+		p = process_tree(commit->tree, p, NULL, "");
+		show_commit(commit);
+	}
+	for (pending = revs->pending_objects; pending; pending = pending->next) {
+		struct object *obj = pending->item;
+		const char *name = pending->name;
+		if (obj->flags & (UNINTERESTING | SEEN))
+			continue;
+		if (obj->type == tag_type) {
+			obj->flags |= SEEN;
+			p = add_object(obj, p, NULL, name);
+			continue;
+		}
+		if (obj->type == tree_type) {
+			p = process_tree((struct tree *)obj, p, NULL, name);
+			continue;
+		}
+		if (obj->type == blob_type) {
+			p = process_blob((struct blob *)obj, p, NULL, name);
+			continue;
+		}
+		die("unknown pending object %s (%s)", sha1_to_hex(obj->sha1), name);
+	}
+	while (objects) {
+		/* An object with name "foo\n0000000..." can be used to
+		 * confuse downstream git-pack-objects very badly.
+		 */
+		const char *ep = strchr(objects->name, '\n');
+		if (ep) {
+			printf("%s %.*s\n", sha1_to_hex(objects->item->sha1),
+			       (int) (ep - objects->name),
+			       objects->name);
+		}
+		else
+			printf("%s %s\n", sha1_to_hex(objects->item->sha1), objects->name);
+		objects = objects->next;
+	}
+}
+
+/*
+ * This is a truly stupid algorithm, but it's only
+ * used for bisection, and we just don't care enough.
+ *
+ * We care just barely enough to avoid recursing for
+ * non-merge entries.
+ */
+static int count_distance(struct commit_list *entry)
+{
+	int nr = 0;
+
+	while (entry) {
+		struct commit *commit = entry->item;
+		struct commit_list *p;
+
+		if (commit->object.flags & (UNINTERESTING | COUNTED))
+			break;
+		if (!revs.prune_fn || (commit->object.flags & TREECHANGE))
+			nr++;
+		commit->object.flags |= COUNTED;
+		p = commit->parents;
+		entry = p;
+		if (p) {
+			p = p->next;
+			while (p) {
+				nr += count_distance(p);
+				p = p->next;
+			}
+		}
+	}
+
+	return nr;
+}
+
+static void clear_distance(struct commit_list *list)
+{
+	while (list) {
+		struct commit *commit = list->item;
+		commit->object.flags &= ~COUNTED;
+		list = list->next;
+	}
+}
+
+static struct commit_list *find_bisection(struct commit_list *list)
+{
+	int nr, closest;
+	struct commit_list *p, *best;
+
+	nr = 0;
+	p = list;
+	while (p) {
+		if (!revs.prune_fn || (p->item->object.flags & TREECHANGE))
+			nr++;
+		p = p->next;
+	}
+	closest = 0;
+	best = list;
+
+	for (p = list; p; p = p->next) {
+		int distance;
+
+		if (revs.prune_fn && !(p->item->object.flags & TREECHANGE))
+			continue;
+
+		distance = count_distance(p);
+		clear_distance(list);
+		if (nr - distance < distance)
+			distance = nr - distance;
+		if (distance > closest) {
+			best = p;
+			closest = distance;
+		}
+	}
+	if (best)
+		best->next = NULL;
+	return best;
+}
+
+static void mark_edge_parents_uninteresting(struct commit *commit)
+{
+	struct commit_list *parents;
+
+	for (parents = commit->parents; parents; parents = parents->next) {
+		struct commit *parent = parents->item;
+		if (!(parent->object.flags & UNINTERESTING))
+			continue;
+		mark_tree_uninteresting(parent->tree);
+		if (revs.edge_hint && !(parent->object.flags & SHOWN)) {
+			parent->object.flags |= SHOWN;
+			printf("-%s\n", sha1_to_hex(parent->object.sha1));
+		}
+	}
+}
+
+static void mark_edges_uninteresting(struct commit_list *list)
+{
+	for ( ; list; list = list->next) {
+		struct commit *commit = list->item;
+
+		if (commit->object.flags & UNINTERESTING) {
+			mark_tree_uninteresting(commit->tree);
+			continue;
+		}
+		mark_edge_parents_uninteresting(commit);
+	}
+}
+
+int cmd_rev_list(int argc, const char **argv, char **envp)
+{
+	struct commit_list *list;
+	int i;
+
+	init_revisions(&revs);
+	revs.abbrev = 0;
+	revs.commit_format = CMIT_FMT_UNSPECIFIED;
+	argc = setup_revisions(argc, argv, &revs, NULL);
+
+	for (i = 1 ; i < argc; i++) {
+		const char *arg = argv[i];
+
+		if (!strcmp(arg, "--header")) {
+			revs.verbose_header = 1;
+			continue;
+		}
+		if (!strcmp(arg, "--timestamp")) {
+			show_timestamp = 1;
+			continue;
+		}
+		if (!strcmp(arg, "--bisect")) {
+			bisect_list = 1;
+			continue;
+		}
+		usage(rev_list_usage);
+
+	}
+	if (revs.commit_format != CMIT_FMT_UNSPECIFIED) {
+		/* The command line has a --pretty  */
+		hdr_termination = '\n';
+		if (revs.commit_format == CMIT_FMT_ONELINE)
+			header_prefix = "";
+		else
+			header_prefix = "commit ";
+	}
+	else if (revs.verbose_header)
+		/* Only --header was specified */
+		revs.commit_format = CMIT_FMT_RAW;
+
+	list = revs.commits;
+
+	if ((!list &&
+	     (!(revs.tag_objects||revs.tree_objects||revs.blob_objects) &&
+	      !revs.pending_objects)) ||
+	    revs.diff)
+		usage(rev_list_usage);
+
+	save_commit_buffer = revs.verbose_header;
+	track_object_refs = 0;
+	if (bisect_list)
+		revs.limited = 1;
+
+	prepare_revision_walk(&revs);
+	if (revs.tree_objects)
+		mark_edges_uninteresting(revs.commits);
+
+	if (bisect_list)
+		revs.commits = find_bisection(revs.commits);
+
+	show_commit_list(&revs);
+
+	return 0;
+}
diff --git a/builtin.h b/builtin.h
index 7744f7d2f6..60541262c4 100644
--- a/builtin.h
+++ b/builtin.h
@@ -24,5 +24,8 @@ extern int cmd_count_objects(int argc, const char **argv, char **envp);
 
 extern int cmd_push(int argc, const char **argv, char **envp);
 extern int cmd_grep(int argc, const char **argv, char **envp);
+extern int cmd_rev_list(int argc, const char **argv, char **envp);
+extern int cmd_check_ref_format(int argc, const char **argv, char **envp);
+extern int cmd_init_db(int argc, const char **argv, char **envp);
 
 #endif
diff --git a/cache.h b/cache.h
index 4b7a439253..afa8e4f0ac 100644
--- a/cache.h
+++ b/cache.h
@@ -158,6 +158,12 @@ extern int index_pipe(unsigned char *sha1, int fd, const char *type, int write_o
 extern int index_path(unsigned char *sha1, const char *path, struct stat *st, int write_object);
 extern void fill_stat_cache_info(struct cache_entry *ce, struct stat *st);
 
+#define REFRESH_REALLY		0x0001	/* ignore_valid */
+#define REFRESH_UNMERGED	0x0002	/* allow unmerged */
+#define REFRESH_QUIET		0x0004	/* be quiet about it */
+#define REFRESH_IGNORE_MISSING	0x0008	/* ignore non-existent */
+extern int refresh_cache(unsigned int flags);
+
 struct cache_file {
 	struct cache_file *next;
 	char lockfile[PATH_MAX];
diff --git a/check-ref-format.c b/check-ref-format.c
deleted file mode 100644
index a0adb3dcb3..0000000000
--- a/check-ref-format.c
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * GIT - The information manager from hell
- */
-
-#include "cache.h"
-#include "refs.h"
-
-#include <stdio.h>
-
-int main(int ac, char **av)
-{
-	if (ac != 2)
-		usage("git-check-ref-format refname");
-	if (check_ref_format(av[1]))
-		exit(1);
-	return 0;
-}
diff --git a/commit.c b/commit.c
index 2717dd81c3..4a26070c13 100644
--- a/commit.c
+++ b/commit.c
@@ -22,23 +22,33 @@ struct sort_node
 
 const char *commit_type = "commit";
 
+struct cmt_fmt_map {
+	const char *n;
+	size_t cmp_len;
+	enum cmit_fmt v;
+} cmt_fmts[] = {
+	{ "raw",	1,	CMIT_FMT_RAW },
+	{ "medium",	1,	CMIT_FMT_MEDIUM },
+	{ "short",	1,	CMIT_FMT_SHORT },
+	{ "full",	5,	CMIT_FMT_FULL },
+	{ "fuller",	5,	CMIT_FMT_FULLER },
+	{ "oneline",	1,	CMIT_FMT_ONELINE },
+};
+
 enum cmit_fmt get_commit_format(const char *arg)
 {
-	if (!*arg)
+	int i;
+
+	if (!arg || !*arg)
 		return CMIT_FMT_DEFAULT;
-	if (!strcmp(arg, "=raw"))
-		return CMIT_FMT_RAW;
-	if (!strcmp(arg, "=medium"))
-		return CMIT_FMT_MEDIUM;
-	if (!strcmp(arg, "=short"))
-		return CMIT_FMT_SHORT;
-	if (!strcmp(arg, "=full"))
-		return CMIT_FMT_FULL;
-	if (!strcmp(arg, "=fuller"))
-		return CMIT_FMT_FULLER;
-	if (!strcmp(arg, "=oneline"))
-		return CMIT_FMT_ONELINE;
-	die("invalid --pretty format");
+	if (*arg == '=')
+		arg++;
+	for (i = 0; i < ARRAY_SIZE(cmt_fmts); i++) {
+		if (!strncmp(arg, cmt_fmts[i].n, cmt_fmts[i].cmp_len))
+			return cmt_fmts[i].v;
+	}
+
+	die("invalid --pretty format: %s", arg);
 }
 
 static struct commit *check_commit(struct object *obj,
diff --git a/diff-tree.c b/diff-tree.c
index 7207867a74..69bb74b310 100644
--- a/diff-tree.c
+++ b/diff-tree.c
@@ -138,7 +138,10 @@ int main(int argc, const char **argv)
 		opt->diffopt.setup |= (DIFF_SETUP_USE_SIZE_CACHE |
 				       DIFF_SETUP_USE_CACHE);
 	while (fgets(line, sizeof(line), stdin))
-		diff_tree_stdin(line);
+		if (line[0] == '\n')
+			fflush(stdout);
+		else
+			diff_tree_stdin(line);
 
 	return 0;
 }
diff --git a/git-am.sh b/git-am.sh
index 33f208cb0b..97ec2d0c7d 100755
--- a/git-am.sh
+++ b/git-am.sh
@@ -59,46 +59,12 @@ fall_back_3way () {
 	GIT_INDEX_FILE="$dotest/patch-merge-tmp-index" \
 	git-write-tree >"$dotest/patch-merge-base+" &&
 	# index has the base tree now.
-	(
-	    cd "$dotest/patch-merge-tmp-dir" &&
-	    GIT_INDEX_FILE="../patch-merge-tmp-index" \
-	    GIT_OBJECT_DIRECTORY="$O_OBJECT" \
-	    git-apply $binary --index <../patch
-        )
+	GIT_INDEX_FILE="$dotest/patch-merge-tmp-index" \
+	git-apply $binary --cached <"$dotest/patch"
     then
 	echo Using index info to reconstruct a base tree...
 	mv "$dotest/patch-merge-base+" "$dotest/patch-merge-base"
 	mv "$dotest/patch-merge-tmp-index" "$dotest/patch-merge-index"
-    else
-	# Otherwise, try nearby trees that can be used to apply the
-	# patch.
-	(
-	    N=10
-
-	    # Hoping the patch is against our recent commits...
-	    git-rev-list --max-count=$N HEAD
-
-	    # or hoping the patch is against known tags...
-	    git-ls-remote --tags .
-	) |
-	while read base junk
-	do
-	    # See if we have it as a tree...
-	    git-cat-file tree "$base" >/dev/null 2>&1 || continue
-
-	    rm -fr "$dotest"/patch-merge-* &&
-	    mkdir "$dotest/patch-merge-tmp-dir" || break
-	    (
-		cd "$dotest/patch-merge-tmp-dir" &&
-		GIT_INDEX_FILE=../patch-merge-tmp-index &&
-		GIT_OBJECT_DIRECTORY="$O_OBJECT" &&
-		export GIT_INDEX_FILE GIT_OBJECT_DIRECTORY &&
-		git-read-tree "$base" &&
-		git-apply $binary --index &&
-		mv ../patch-merge-tmp-index ../patch-merge-index &&
-		echo "$base" >../patch-merge-base
-	    ) <"$dotest/patch"  2>/dev/null && break
-	done
     fi
 
     test -f "$dotest/patch-merge-index" &&
diff --git a/git-cvsimport.perl b/git-cvsimport.perl
index c0ae00bda7..8c707f2c66 100755
--- a/git-cvsimport.perl
+++ b/git-cvsimport.perl
@@ -350,7 +350,7 @@ sub _line {
 				return $res;
 			} elsif($line =~ s/^E //) {
 				# print STDERR "S: $line\n";
-			} elsif($line =~ /^Remove-entry /i) {
+			} elsif($line =~ /^(Remove-entry|Removed) /i) {
 				$line = $self->readline(); # filename
 				$line = $self->readline(); # OK
 				chomp $line;
diff --git a/git-quiltimport.sh b/git-quiltimport.sh
new file mode 100755
index 0000000000..12d9d0cbc9
--- /dev/null
+++ b/git-quiltimport.sh
@@ -0,0 +1,118 @@
+#!/bin/sh
+USAGE='--dry-run --author <author> --patches </path/to/quilt/patch/directory>'
+SUBDIRECTORY_ON=Yes
+. git-sh-setup
+
+dry_run=""
+quilt_author=""
+while case "$#" in 0) break;; esac
+do
+	case "$1" in
+	--au=*|--aut=*|--auth=*|--autho=*|--author=*)
+		quilt_author=$(expr "$1" : '-[^=]*\(.*\)')
+		shift
+		;;
+
+	--au|--aut|--auth|--autho|--author)
+		case "$#" in 1) usage ;; esac
+		shift
+		quilt_author="$1"
+		shift
+		;;
+
+	--dry-run)
+		shift
+		dry_run=1
+		;;
+
+	--pa=*|--pat=*|--patc=*|--patch=*|--patche=*|--patches=*)
+		QUILT_PATCHES=$(expr "$1" : '-[^=]*\(.*\)')
+		shift
+		;;
+
+	--pa|--pat|--patc|--patch|--patche|--patches)
+		case "$#" in 1) usage ;; esac
+		shift
+		QUILT_PATCHES="$1"
+		shift
+		;;
+
+	*)
+		break
+		;;
+	esac
+done
+
+# Quilt Author
+if [ -n "$quilt_author" ] ; then
+	quilt_author_name=$(expr "z$quilt_author" : 'z\(.*[^ ]\) *<.*') &&
+	quilt_author_email=$(expr "z$quilt_author" : '.*<\([^>]*\)') &&
+	test '' != "$quilt_author_name" &&
+	test '' != "$quilt_author_email" ||
+	die "malformatted --author parameter"
+fi
+
+# Quilt patch directory
+: ${QUILT_PATCHES:=patches}
+if ! [ -d "$QUILT_PATCHES" ] ; then
+	echo "The \"$QUILT_PATCHES\" directory does not exist."
+	exit 1
+fi
+
+# Temporay directories
+tmp_dir=.dotest
+tmp_msg="$tmp_dir/msg"
+tmp_patch="$tmp_dir/patch"
+tmp_info="$tmp_dir/info"
+
+
+# Find the intial commit
+commit=$(git-rev-parse HEAD)
+
+mkdir $tmp_dir || exit 2
+for patch_name in $(cat "$QUILT_PATCHES/series" | grep -v '^#'); do
+	echo $patch_name
+	(cat $QUILT_PATCHES/$patch_name | git-mailinfo "$tmp_msg" "$tmp_patch" > "$tmp_info") || exit 3
+
+	# Parse the author information
+	export GIT_AUTHOR_NAME=$(sed -ne 's/Author: //p' "$tmp_info")
+	export GIT_AUTHOR_EMAIL=$(sed -ne 's/Email: //p' "$tmp_info")
+	while test -z "$GIT_AUTHOR_EMAIL" && test -z "$GIT_AUTHOR_NAME" ; do
+		if [ -n "$quilt_author" ] ; then
+			GIT_AUTHOR_NAME="$quilt_author_name";
+			GIT_AUTHOR_EMAIL="$quilt_author_email";
+		elif [ -n "$dry_run" ]; then
+			echo "No author found in $patch_name" >&2;
+			GIT_AUTHOR_NAME="dry-run-not-found";
+			GIT_AUTHOR_EMAIL="dry-run-not-found";
+		else
+			echo "No author found in $patch_name" >&2;
+			echo "---"
+			cat $tmp_msg
+			echo -n "Author: ";
+			read patch_author
+
+			echo "$patch_author"
+
+			patch_author_name=$(expr "z$patch_author" : 'z\(.*[^ ]\) *<.*') &&
+			patch_author_email=$(expr "z$patch_author" : '.*<\([^>]*\)') &&
+			test '' != "$patch_author_name" &&
+			test '' != "$patch_author_email" &&
+			GIT_AUTHOR_NAME="$patch_author_name" &&
+			GIT_AUTHOR_EMAIL="$patch_author_email"
+		fi
+	done
+	export GIT_AUTHOR_DATE=$(sed -ne 's/Date: //p' "$tmp_info")
+	export SUBJECT=$(sed -ne 's/Subject: //p' "$tmp_info")
+	if [ -z "$SUBJECT" ] ; then
+		SUBJECT=$(echo $patch_name | sed -e 's/.patch$//')
+	fi
+
+	if [ -z "$dry_run" ] ; then
+		git-apply --index -C1 "$tmp_patch" &&
+		tree=$(git-write-tree) &&
+		commit=$((echo "$SUBJECT"; echo; cat "$tmp_msg") | git-commit-tree $tree -p $commit) &&
+		git-update-ref HEAD $commit || exit 4
+	fi
+done
+rm -rf $tmp_dir || exit 5
diff --git a/git.c b/git.c
index a94d9ee5a7..3216d311b2 100644
--- a/git.c
+++ b/git.c
@@ -50,6 +50,9 @@ static void handle_internal_command(int argc, const char **argv, char **envp)
 		{ "count-objects", cmd_count_objects },
 		{ "diff", cmd_diff },
 		{ "grep", cmd_grep },
+		{ "rev-list", cmd_rev_list },
+		{ "init-db", cmd_init_db },
+		{ "check-ref-format", cmd_check_ref_format }
 	};
 	int i;
 
diff --git a/init-db.c b/init-db.c
deleted file mode 100644
index ff294960f2..0000000000
--- a/init-db.c
+++ /dev/null
@@ -1,291 +0,0 @@
-/*
- * GIT - The information manager from hell
- *
- * Copyright (C) Linus Torvalds, 2005
- */
-#include "cache.h"
-
-#ifndef DEFAULT_GIT_TEMPLATE_DIR
-#define DEFAULT_GIT_TEMPLATE_DIR "/usr/share/git-core/templates/"
-#endif
-
-static void safe_create_dir(const char *dir, int share)
-{
-	if (mkdir(dir, 0777) < 0) {
-		if (errno != EEXIST) {
-			perror(dir);
-			exit(1);
-		}
-	}
-	else if (share && adjust_shared_perm(dir))
-		die("Could not make %s writable by group\n", dir);
-}
-
-static int copy_file(const char *dst, const char *src, int mode)
-{
-	int fdi, fdo, status;
-
-	mode = (mode & 0111) ? 0777 : 0666;
-	if ((fdi = open(src, O_RDONLY)) < 0)
-		return fdi;
-	if ((fdo = open(dst, O_WRONLY | O_CREAT | O_EXCL, mode)) < 0) {
-		close(fdi);
-		return fdo;
-	}
-	status = copy_fd(fdi, fdo);
-	close(fdo);
-
-	if (!status && adjust_shared_perm(dst))
-		return -1;
-
-	return status;
-}
-
-static void copy_templates_1(char *path, int baselen,
-			     char *template, int template_baselen,
-			     DIR *dir)
-{
-	struct dirent *de;
-
-	/* Note: if ".git/hooks" file exists in the repository being
-	 * re-initialized, /etc/core-git/templates/hooks/update would
-	 * cause git-init-db to fail here.  I think this is sane but
-	 * it means that the set of templates we ship by default, along
-	 * with the way the namespace under .git/ is organized, should
-	 * be really carefully chosen.
-	 */
-	safe_create_dir(path, 1);
-	while ((de = readdir(dir)) != NULL) {
-		struct stat st_git, st_template;
-		int namelen;
-		int exists = 0;
-
-		if (de->d_name[0] == '.')
-			continue;
-		namelen = strlen(de->d_name);
-		if ((PATH_MAX <= baselen + namelen) ||
-		    (PATH_MAX <= template_baselen + namelen))
-			die("insanely long template name %s", de->d_name);
-		memcpy(path + baselen, de->d_name, namelen+1);
-		memcpy(template + template_baselen, de->d_name, namelen+1);
-		if (lstat(path, &st_git)) {
-			if (errno != ENOENT)
-				die("cannot stat %s", path);
-		}
-		else
-			exists = 1;
-
-		if (lstat(template, &st_template))
-			die("cannot stat template %s", template);
-
-		if (S_ISDIR(st_template.st_mode)) {
-			DIR *subdir = opendir(template);
-			int baselen_sub = baselen + namelen;
-			int template_baselen_sub = template_baselen + namelen;
-			if (!subdir)
-				die("cannot opendir %s", template);
-			path[baselen_sub++] =
-				template[template_baselen_sub++] = '/';
-			path[baselen_sub] =
-				template[template_baselen_sub] = 0;
-			copy_templates_1(path, baselen_sub,
-					 template, template_baselen_sub,
-					 subdir);
-			closedir(subdir);
-		}
-		else if (exists)
-			continue;
-		else if (S_ISLNK(st_template.st_mode)) {
-			char lnk[256];
-			int len;
-			len = readlink(template, lnk, sizeof(lnk));
-			if (len < 0)
-				die("cannot readlink %s", template);
-			if (sizeof(lnk) <= len)
-				die("insanely long symlink %s", template);
-			lnk[len] = 0;
-			if (symlink(lnk, path))
-				die("cannot symlink %s %s", lnk, path);
-		}
-		else if (S_ISREG(st_template.st_mode)) {
-			if (copy_file(path, template, st_template.st_mode))
-				die("cannot copy %s to %s", template, path);
-		}
-		else
-			error("ignoring template %s", template);
-	}
-}
-
-static void copy_templates(const char *git_dir, int len, char *template_dir)
-{
-	char path[PATH_MAX];
-	char template_path[PATH_MAX];
-	int template_len;
-	DIR *dir;
-
-	if (!template_dir)
-		template_dir = DEFAULT_GIT_TEMPLATE_DIR;
-	strcpy(template_path, template_dir);
-	template_len = strlen(template_path);
-	if (template_path[template_len-1] != '/') {
-		template_path[template_len++] = '/';
-		template_path[template_len] = 0;
-	}
-	dir = opendir(template_path);
-	if (!dir) {
-		fprintf(stderr, "warning: templates not found %s\n",
-			template_dir);
-		return;
-	}
-
-	/* Make sure that template is from the correct vintage */
-	strcpy(template_path + template_len, "config");
-	repository_format_version = 0;
-	git_config_from_file(check_repository_format_version,
-			     template_path);
-	template_path[template_len] = 0;
-
-	if (repository_format_version &&
-	    repository_format_version != GIT_REPO_VERSION) {
-		fprintf(stderr, "warning: not copying templates of "
-			"a wrong format version %d from '%s'\n",
-			repository_format_version,
-			template_dir);
-		closedir(dir);
-		return;
-	}
-
-	memcpy(path, git_dir, len);
-	path[len] = 0;
-	copy_templates_1(path, len,
-			 template_path, template_len,
-			 dir);
-	closedir(dir);
-}
-
-static void create_default_files(const char *git_dir, char *template_path)
-{
-	unsigned len = strlen(git_dir);
-	static char path[PATH_MAX];
-	unsigned char sha1[20];
-	struct stat st1;
-	char repo_version_string[10];
-
-	if (len > sizeof(path)-50)
-		die("insane git directory %s", git_dir);
-	memcpy(path, git_dir, len);
-
-	if (len && path[len-1] != '/')
-		path[len++] = '/';
-
-	/*
-	 * 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);
-
-	/* 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);
-
-	git_config(git_default_config);
-
-	/*
-	 * Create the default symlink from ".git/HEAD" to the "master"
-	 * branch, if it does not exist yet.
-	 */
-	strcpy(path + len, "HEAD");
-	if (read_ref(path, sha1) < 0) {
-		if (create_symref(path, "refs/heads/master") < 0)
-			exit(1);
-	}
-
-	/* This forces creation of new config file */
-	sprintf(repo_version_string, "%d", GIT_REPO_VERSION);
-	git_config_set("core.repositoryformatversion", repo_version_string);
-
-	path[len] = 0;
-	strcpy(path + len, "config");
-
-	/* Check filemode trustability */
-	if (!lstat(path, &st1)) {
-		struct stat st2;
-		int filemode = (!chmod(path, st1.st_mode ^ S_IXUSR) &&
-				!lstat(path, &st2) &&
-				st1.st_mode != st2.st_mode);
-		git_config_set("core.filemode",
-			       filemode ? "true" : "false");
-	}
-}
-
-static const char init_db_usage[] =
-"git-init-db [--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 main(int argc, char **argv)
-{
-	const char *git_dir;
-	const char *sha1_dir;
-	char *path, *template_dir = NULL;
-	int len, i;
-
-	for (i = 1; i < argc; i++, argv++) {
-		char *arg = argv[1];
-		if (!strncmp(arg, "--template=", 11))
-			template_dir = arg+11;
-		else if (!strcmp(arg, "--shared"))
-			shared_repository = 1;
-		else
-			die(init_db_usage);
-	}
-
-	/*
-	 * Set up the default .git directory contents
-	 */
-	git_dir = getenv(GIT_DIR_ENVIRONMENT);
-	if (!git_dir) {
-		git_dir = DEFAULT_GIT_DIR_ENVIRONMENT;
-		fprintf(stderr, "defaulting to local storage area\n");
-	}
-	safe_create_dir(git_dir, 0);
-
-	/* Check to see if the repository version is right.
-	 * Note that a newly created repository does not have
-	 * config file, so this will not fail.  What we are catching
-	 * is an attempt to reinitialize new repository with an old tool.
-	 */
-	check_repository_format();
-
-	create_default_files(git_dir, template_dir);
-
-	/*
-	 * And set up the object store.
-	 */
-	sha1_dir = get_object_directory();
-	len = strlen(sha1_dir);
-	path = xmalloc(len + 40);
-	memcpy(path, sha1_dir, len);
-
-	safe_create_dir(sha1_dir, 1);
-	strcpy(path+len, "/pack");
-	safe_create_dir(path, 1);
-	strcpy(path+len, "/info");
-	safe_create_dir(path, 1);
-
-	if (shared_repository)
-		git_config_set("core.sharedRepository", "true");
-
-	return 0;
-}
diff --git a/read-cache.c b/read-cache.c
index a917ab0cfe..b95edcc14c 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -496,6 +496,123 @@ int add_cache_entry(struct cache_entry *ce, int option)
 	return 0;
 }
 
+/* Three functions to allow overloaded pointer return; see linux/err.h */
+static inline void *ERR_PTR(long error)
+{
+	return (void *) error;
+}
+
+static inline long PTR_ERR(const void *ptr)
+{
+	return (long) ptr;
+}
+
+static inline long IS_ERR(const void *ptr)
+{
+	return (unsigned long)ptr > (unsigned long)-1000L;
+}
+
+/*
+ * "refresh" does not calculate a new sha1 file or bring the
+ * cache up-to-date for mode/content changes. But what it
+ * _does_ do is to "re-match" the stat information of a file
+ * with the cache, so that you can refresh the cache for a
+ * file that hasn't been changed but where the stat entry is
+ * out of date.
+ *
+ * For example, you'd want to do this after doing a "git-read-tree",
+ * to link up the stat cache details with the proper files.
+ */
+static struct cache_entry *refresh_entry(struct cache_entry *ce, int really)
+{
+	struct stat st;
+	struct cache_entry *updated;
+	int changed, size;
+
+	if (lstat(ce->name, &st) < 0)
+		return ERR_PTR(-errno);
+
+	changed = ce_match_stat(ce, &st, really);
+	if (!changed) {
+		if (really && assume_unchanged &&
+		    !(ce->ce_flags & htons(CE_VALID)))
+			; /* mark this one VALID again */
+		else
+			return NULL;
+	}
+
+	if (ce_modified(ce, &st, really))
+		return ERR_PTR(-EINVAL);
+
+	size = ce_size(ce);
+	updated = xmalloc(size);
+	memcpy(updated, ce, size);
+	fill_stat_cache_info(updated, &st);
+
+	/* In this case, if really is not set, we should leave
+	 * CE_VALID bit alone.  Otherwise, paths marked with
+	 * --no-assume-unchanged (i.e. things to be edited) will
+	 * reacquire CE_VALID bit automatically, which is not
+	 * really what we want.
+	 */
+	if (!really && assume_unchanged && !(ce->ce_flags & htons(CE_VALID)))
+		updated->ce_flags &= ~htons(CE_VALID);
+
+	return updated;
+}
+
+int refresh_cache(unsigned int flags)
+{
+	int i;
+	int has_errors = 0;
+	int really = (flags & REFRESH_REALLY) != 0;
+	int allow_unmerged = (flags & REFRESH_UNMERGED) != 0;
+	int quiet = (flags & REFRESH_QUIET) != 0;
+	int not_new = (flags & REFRESH_IGNORE_MISSING) != 0;
+
+	for (i = 0; i < active_nr; i++) {
+		struct cache_entry *ce, *new;
+		ce = active_cache[i];
+		if (ce_stage(ce)) {
+			while ((i < active_nr) &&
+			       ! strcmp(active_cache[i]->name, ce->name))
+				i++;
+			i--;
+			if (allow_unmerged)
+				continue;
+			printf("%s: needs merge\n", ce->name);
+			has_errors = 1;
+			continue;
+		}
+
+		new = refresh_entry(ce, really);
+		if (!new)
+			continue;
+		if (IS_ERR(new)) {
+			if (not_new && PTR_ERR(new) == -ENOENT)
+				continue;
+			if (really && PTR_ERR(new) == -EINVAL) {
+				/* If we are doing --really-refresh that
+				 * means the index is not valid anymore.
+				 */
+				ce->ce_flags &= ~htons(CE_VALID);
+				active_cache_changed = 1;
+			}
+			if (quiet)
+				continue;
+			printf("%s: needs update\n", ce->name);
+			has_errors = 1;
+			continue;
+		}
+		active_cache_changed = 1;
+		/* You can NOT just free active_cache[i] here, since it
+		 * might not be necessarily malloc()ed but can also come
+		 * from mmap(). */
+		active_cache[i] = new;
+	}
+	return has_errors;
+}
+
 static int verify_hdr(struct cache_header *hdr, unsigned long size)
 {
 	SHA_CTX c;
diff --git a/refs.c b/refs.c
index 6c91ae6468..0f3491f871 100644
--- a/refs.c
+++ b/refs.c
@@ -220,12 +220,9 @@ static char *ref_lock_file_name(const char *ref)
 
 int get_ref_sha1(const char *ref, unsigned char *sha1)
 {
-	const char *filename;
-
 	if (check_ref_format(ref))
 		return -1;
-	filename = git_path("refs/%s", ref);
-	return read_ref(filename, sha1);
+	return read_ref(git_path("refs/%s", ref), sha1);
 }
 
 static int lock_ref_file(const char *filename, const char *lock_filename,
diff --git a/rev-list.c b/rev-list.c
deleted file mode 100644
index 8b0ec388fa..0000000000
--- a/rev-list.c
+++ /dev/null
@@ -1,357 +0,0 @@
-#include "cache.h"
-#include "refs.h"
-#include "tag.h"
-#include "commit.h"
-#include "tree.h"
-#include "blob.h"
-#include "tree-walk.h"
-#include "diff.h"
-#include "revision.h"
-
-/* bits #0-15 in revision.h */
-
-#define COUNTED		(1u<<16)
-
-static const char rev_list_usage[] =
-"git-rev-list [OPTION] <commit-id>... [ -- paths... ]\n"
-"  limiting output:\n"
-"    --max-count=nr\n"
-"    --max-age=epoch\n"
-"    --min-age=epoch\n"
-"    --sparse\n"
-"    --no-merges\n"
-"    --remove-empty\n"
-"    --all\n"
-"  ordering output:\n"
-"    --topo-order\n"
-"    --date-order\n"
-"  formatting output:\n"
-"    --parents\n"
-"    --objects | --objects-edge\n"
-"    --unpacked\n"
-"    --header | --pretty\n"
-"    --abbrev=nr | --no-abbrev\n"
-"    --abbrev-commit\n"
-"  special purpose:\n"
-"    --bisect"
-;
-
-struct rev_info revs;
-
-static int bisect_list = 0;
-static int show_timestamp = 0;
-static int hdr_termination = 0;
-static const char *header_prefix;
-
-static void show_commit(struct commit *commit)
-{
-	if (show_timestamp)
-		printf("%lu ", commit->date);
-	if (header_prefix)
-		fputs(header_prefix, stdout);
-	if (commit->object.flags & BOUNDARY)
-		putchar('-');
-	if (revs.abbrev_commit && revs.abbrev)
-		fputs(find_unique_abbrev(commit->object.sha1, revs.abbrev),
-		      stdout);
-	else
-		fputs(sha1_to_hex(commit->object.sha1), stdout);
-	if (revs.parents) {
-		struct commit_list *parents = commit->parents;
-		while (parents) {
-			struct object *o = &(parents->item->object);
-			parents = parents->next;
-			if (o->flags & TMP_MARK)
-				continue;
-			printf(" %s", sha1_to_hex(o->sha1));
-			o->flags |= TMP_MARK;
-		}
-		/* TMP_MARK is a general purpose flag that can
-		 * be used locally, but the user should clean
-		 * things up after it is done with them.
-		 */
-		for (parents = commit->parents;
-		     parents;
-		     parents = parents->next)
-			parents->item->object.flags &= ~TMP_MARK;
-	}
-	if (revs.commit_format == CMIT_FMT_ONELINE)
-		putchar(' ');
-	else
-		putchar('\n');
-
-	if (revs.verbose_header) {
-		static char pretty_header[16384];
-		pretty_print_commit(revs.commit_format, commit, ~0,
-				    pretty_header, sizeof(pretty_header),
-				    revs.abbrev);
-		printf("%s%c", pretty_header, hdr_termination);
-	}
-	fflush(stdout);
-}
-
-static struct object_list **process_blob(struct blob *blob,
-					 struct object_list **p,
-					 struct name_path *path,
-					 const char *name)
-{
-	struct object *obj = &blob->object;
-
-	if (!revs.blob_objects)
-		return p;
-	if (obj->flags & (UNINTERESTING | SEEN))
-		return p;
-	obj->flags |= SEEN;
-	return add_object(obj, p, path, name);
-}
-
-static struct object_list **process_tree(struct tree *tree,
-					 struct object_list **p,
-					 struct name_path *path,
-					 const char *name)
-{
-	struct object *obj = &tree->object;
-	struct tree_entry_list *entry;
-	struct name_path me;
-
-	if (!revs.tree_objects)
-		return p;
-	if (obj->flags & (UNINTERESTING | SEEN))
-		return p;
-	if (parse_tree(tree) < 0)
-		die("bad tree object %s", sha1_to_hex(obj->sha1));
-	obj->flags |= SEEN;
-	p = add_object(obj, p, path, name);
-	me.up = path;
-	me.elem = name;
-	me.elem_len = strlen(name);
-	entry = tree->entries;
-	tree->entries = NULL;
-	while (entry) {
-		struct tree_entry_list *next = entry->next;
-		if (entry->directory)
-			p = process_tree(entry->item.tree, p, &me, entry->name);
-		else
-			p = process_blob(entry->item.blob, p, &me, entry->name);
-		free(entry);
-		entry = next;
-	}
-	return p;
-}
-
-static void show_commit_list(struct rev_info *revs)
-{
-	struct commit *commit;
-	struct object_list *objects = NULL, **p = &objects, *pending;
-
-	while ((commit = get_revision(revs)) != NULL) {
-		p = process_tree(commit->tree, p, NULL, "");
-		show_commit(commit);
-	}
-	for (pending = revs->pending_objects; pending; pending = pending->next) {
-		struct object *obj = pending->item;
-		const char *name = pending->name;
-		if (obj->flags & (UNINTERESTING | SEEN))
-			continue;
-		if (obj->type == tag_type) {
-			obj->flags |= SEEN;
-			p = add_object(obj, p, NULL, name);
-			continue;
-		}
-		if (obj->type == tree_type) {
-			p = process_tree((struct tree *)obj, p, NULL, name);
-			continue;
-		}
-		if (obj->type == blob_type) {
-			p = process_blob((struct blob *)obj, p, NULL, name);
-			continue;
-		}
-		die("unknown pending object %s (%s)", sha1_to_hex(obj->sha1), name);
-	}
-	while (objects) {
-		/* An object with name "foo\n0000000..." can be used to
-		 * confuse downstream git-pack-objects very badly.
-		 */
-		const char *ep = strchr(objects->name, '\n');
-		if (ep) {
-			printf("%s %.*s\n", sha1_to_hex(objects->item->sha1),
-			       (int) (ep - objects->name),
-			       objects->name);
-		}
-		else
-			printf("%s %s\n", sha1_to_hex(objects->item->sha1), objects->name);
-		objects = objects->next;
-	}
-}
-
-/*
- * This is a truly stupid algorithm, but it's only
- * used for bisection, and we just don't care enough.
- *
- * We care just barely enough to avoid recursing for
- * non-merge entries.
- */
-static int count_distance(struct commit_list *entry)
-{
-	int nr = 0;
-
-	while (entry) {
-		struct commit *commit = entry->item;
-		struct commit_list *p;
-
-		if (commit->object.flags & (UNINTERESTING | COUNTED))
-			break;
-		if (!revs.prune_fn || (commit->object.flags & TREECHANGE))
-			nr++;
-		commit->object.flags |= COUNTED;
-		p = commit->parents;
-		entry = p;
-		if (p) {
-			p = p->next;
-			while (p) {
-				nr += count_distance(p);
-				p = p->next;
-			}
-		}
-	}
-
-	return nr;
-}
-
-static void clear_distance(struct commit_list *list)
-{
-	while (list) {
-		struct commit *commit = list->item;
-		commit->object.flags &= ~COUNTED;
-		list = list->next;
-	}
-}
-
-static struct commit_list *find_bisection(struct commit_list *list)
-{
-	int nr, closest;
-	struct commit_list *p, *best;
-
-	nr = 0;
-	p = list;
-	while (p) {
-		if (!revs.prune_fn || (p->item->object.flags & TREECHANGE))
-			nr++;
-		p = p->next;
-	}
-	closest = 0;
-	best = list;
-
-	for (p = list; p; p = p->next) {
-		int distance;
-
-		if (revs.prune_fn && !(p->item->object.flags & TREECHANGE))
-			continue;
-
-		distance = count_distance(p);
-		clear_distance(list);
-		if (nr - distance < distance)
-			distance = nr - distance;
-		if (distance > closest) {
-			best = p;
-			closest = distance;
-		}
-	}
-	if (best)
-		best->next = NULL;
-	return best;
-}
-
-static void mark_edge_parents_uninteresting(struct commit *commit)
-{
-	struct commit_list *parents;
-
-	for (parents = commit->parents; parents; parents = parents->next) {
-		struct commit *parent = parents->item;
-		if (!(parent->object.flags & UNINTERESTING))
-			continue;
-		mark_tree_uninteresting(parent->tree);
-		if (revs.edge_hint && !(parent->object.flags & SHOWN)) {
-			parent->object.flags |= SHOWN;
-			printf("-%s\n", sha1_to_hex(parent->object.sha1));
-		}
-	}
-}
-
-static void mark_edges_uninteresting(struct commit_list *list)
-{
-	for ( ; list; list = list->next) {
-		struct commit *commit = list->item;
-
-		if (commit->object.flags & UNINTERESTING) {
-			mark_tree_uninteresting(commit->tree);
-			continue;
-		}
-		mark_edge_parents_uninteresting(commit);
-	}
-}
-
-int main(int argc, const char **argv)
-{
-	struct commit_list *list;
-	int i;
-
-	init_revisions(&revs);
-	revs.abbrev = 0;
-	revs.commit_format = CMIT_FMT_UNSPECIFIED;
-	argc = setup_revisions(argc, argv, &revs, NULL);
-
-	for (i = 1 ; i < argc; i++) {
-		const char *arg = argv[i];
-
-		if (!strcmp(arg, "--header")) {
-			revs.verbose_header = 1;
-			continue;
-		}
-		if (!strcmp(arg, "--timestamp")) {
-			show_timestamp = 1;
-			continue;
-		}
-		if (!strcmp(arg, "--bisect")) {
-			bisect_list = 1;
-			continue;
-		}
-		usage(rev_list_usage);
-
-	}
-	if (revs.commit_format != CMIT_FMT_UNSPECIFIED) {
-		/* The command line has a --pretty  */
-		hdr_termination = '\n';
-		if (revs.commit_format == CMIT_FMT_ONELINE)
-			header_prefix = "";
-		else
-			header_prefix = "commit ";
-	}
-	else if (revs.verbose_header)
-		/* Only --header was specified */
-		revs.commit_format = CMIT_FMT_RAW;
-
-	list = revs.commits;
-
-	if ((!list &&
-	     (!(revs.tag_objects||revs.tree_objects||revs.blob_objects) &&
-	      !revs.pending_objects)) ||
-	    revs.diff)
-		usage(rev_list_usage);
-
-	save_commit_buffer = revs.verbose_header;
-	track_object_refs = 0;
-	if (bisect_list)
-		revs.limited = 1;
-
-	prepare_revision_walk(&revs);
-	if (revs.tree_objects)
-		mark_edges_uninteresting(revs.commits);
-
-	if (bisect_list)
-		revs.commits = find_bisection(revs.commits);
-
-	show_commit_list(&revs);
-
-	return 0;
-}
diff --git a/update-index.c b/update-index.c
index 3d7e02db2c..7d6de821e2 100644
--- a/update-index.c
+++ b/update-index.c
@@ -18,9 +18,6 @@
 static int allow_add;
 static int allow_remove;
 static int allow_replace;
-static int allow_unmerged; /* --refresh needing merge is not error */
-static int not_new; /* --refresh not having working tree files is not error */
-static int quiet; /* --refresh needing update is not error */
 static int info_only;
 static int force_remove;
 static int verbose;
@@ -28,23 +25,6 @@ static int mark_valid_only = 0;
 #define MARK_VALID 1
 #define UNMARK_VALID 2
 
-
-/* Three functions to allow overloaded pointer return; see linux/err.h */
-static inline void *ERR_PTR(long error)
-{
-	return (void *) error;
-}
-
-static inline long PTR_ERR(const void *ptr)
-{
-	return (long) ptr;
-}
-
-static inline long IS_ERR(const void *ptr)
-{
-	return (unsigned long)ptr > (unsigned long)-1000L;
-}
-
 static void report(const char *fmt, ...)
 {
 	va_list vp;
@@ -140,103 +120,6 @@ static int add_file_to_cache(const char *path)
 	return 0;
 }
 
-/*
- * "refresh" does not calculate a new sha1 file or bring the
- * cache up-to-date for mode/content changes. But what it
- * _does_ do is to "re-match" the stat information of a file
- * with the cache, so that you can refresh the cache for a
- * file that hasn't been changed but where the stat entry is
- * out of date.
- *
- * For example, you'd want to do this after doing a "git-read-tree",
- * to link up the stat cache details with the proper files.
- */
-static struct cache_entry *refresh_entry(struct cache_entry *ce, int really)
-{
-	struct stat st;
-	struct cache_entry *updated;
-	int changed, size;
-
-	if (lstat(ce->name, &st) < 0)
-		return ERR_PTR(-errno);
-
-	changed = ce_match_stat(ce, &st, really);
-	if (!changed) {
-		if (really && assume_unchanged &&
-		    !(ce->ce_flags & htons(CE_VALID)))
-			; /* mark this one VALID again */
-		else
-			return NULL;
-	}
-
-	if (ce_modified(ce, &st, really))
-		return ERR_PTR(-EINVAL);
-
-	size = ce_size(ce);
-	updated = xmalloc(size);
-	memcpy(updated, ce, size);
-	fill_stat_cache_info(updated, &st);
-
-	/* In this case, if really is not set, we should leave
-	 * CE_VALID bit alone.  Otherwise, paths marked with
-	 * --no-assume-unchanged (i.e. things to be edited) will
-	 * reacquire CE_VALID bit automatically, which is not
-	 * really what we want.
-	 */
-	if (!really && assume_unchanged && !(ce->ce_flags & htons(CE_VALID)))
-		updated->ce_flags &= ~htons(CE_VALID);
-
-	return updated;
-}
-
-static int refresh_cache(int really)
-{
-	int i;
-	int has_errors = 0;
-
-	for (i = 0; i < active_nr; i++) {
-		struct cache_entry *ce, *new;
-		ce = active_cache[i];
-		if (ce_stage(ce)) {
-			while ((i < active_nr) &&
-			       ! strcmp(active_cache[i]->name, ce->name))
-				i++;
-			i--;
-			if (allow_unmerged)
-				continue;
-			printf("%s: needs merge\n", ce->name);
-			has_errors = 1;
-			continue;
-		}
-
-		new = refresh_entry(ce, really);
-		if (!new)
-			continue;
-		if (IS_ERR(new)) {
-			if (not_new && PTR_ERR(new) == -ENOENT)
-				continue;
-			if (really && PTR_ERR(new) == -EINVAL) {
-				/* If we are doing --really-refresh that
-				 * means the index is not valid anymore.
-				 */
-				ce->ce_flags &= ~htons(CE_VALID);
-				active_cache_changed = 1;
-			}
-			if (quiet)
-				continue;
-			printf("%s: needs update\n", ce->name);
-			has_errors = 1;
-			continue;
-		}
-		active_cache_changed = 1;
-		/* You can NOT just free active_cache[i] here, since it
-		 * might not be necessarily malloc()ed but can also come
-		 * from mmap(). */
-		active_cache[i] = new;
-	}
-	return has_errors;
-}
-
 /*
  * We fundamentally don't like some paths: we don't want
  * dot or dot-dot anywhere, and for obvious reasons don't
@@ -653,6 +536,7 @@ int main(int argc, const char **argv)
 	const char *prefix = setup_git_directory();
 	int prefix_length = prefix ? strlen(prefix) : 0;
 	char set_executable_bit = 0;
+	unsigned int refresh_flags = 0;
 
 	git_config(git_default_config);
 
@@ -673,7 +557,7 @@ int main(int argc, const char **argv)
 				continue;
 			}
 			if (!strcmp(path, "-q")) {
-				quiet = 1;
+				refresh_flags |= REFRESH_QUIET;
 				continue;
 			}
 			if (!strcmp(path, "--add")) {
@@ -689,15 +573,15 @@ int main(int argc, const char **argv)
 				continue;
 			}
 			if (!strcmp(path, "--unmerged")) {
-				allow_unmerged = 1;
+				refresh_flags |= REFRESH_UNMERGED;
 				continue;
 			}
 			if (!strcmp(path, "--refresh")) {
-				has_errors |= refresh_cache(0);
+				has_errors |= refresh_cache(refresh_flags);
 				continue;
 			}
 			if (!strcmp(path, "--really-refresh")) {
-				has_errors |= refresh_cache(1);
+				has_errors |= refresh_cache(REFRESH_REALLY | refresh_flags);
 				continue;
 			}
 			if (!strcmp(path, "--cacheinfo")) {
@@ -770,7 +654,7 @@ int main(int argc, const char **argv)
 				goto finish;
 			}
 			if (!strcmp(path, "--ignore-missing")) {
-				not_new = 1;
+				refresh_flags |= REFRESH_IGNORE_MISSING;
 				continue;
 			}
 			if (!strcmp(path, "--verbose")) {