Merge branch 'js/read-tree' into js/c-merge-recursive

* js/read-tree: (107 commits)
  read-tree: move merge functions to the library
  read-trees: refactor the unpack_trees() part
  tar-tree: illustrate an obscure feature better
  git.c: allow alias expansion without a git directory
  setup_git_directory_gently: do not barf when GIT_DIR is given.
  Build on Debian GNU/kFreeBSD
  Call setup_git_directory() much earlier
  Call setup_git_directory() early
  Display an error from update-ref if target ref name is invalid.
  Fix http-fetch
  t4103: fix binary patch application test.
  git-apply -R: binary patches are irreversible for now.
  Teach git-apply about '-R'
  Makefile: ssh-pull.o depends on ssh-fetch.c
  log and diff family: honor config even from subdirectories
  git-reset: detect update-ref error and report it.
  lost-found: use fsck-objects --full
  Teach git-http-fetch the --stdin switch
  Teach git-local-fetch the --stdin switch
  Make pull() support fetching multiple targets at once
  ...

103 files changed, 2902 insertions, 1668 deletions

diff --git a/.gitignore b/.gitignore
index 52d61f3193..fb0fa3f16a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -137,4 +137,10 @@ git-core.spec
 *.[ao]
 *.py[co]
 config.mak
+autom4te.cache
+config.log
+config.status
+config.mak.in
+config.mak.autogen
+configure
 git-blame
diff --git a/Documentation/Makefile b/Documentation/Makefile
index 2b0efe7921..0d9ffb4ad9 100644
--- a/Documentation/Makefile
+++ b/Documentation/Makefile
@@ -25,10 +25,10 @@ DOC_MAN1=$(patsubst %.txt,%.1,$(MAN1_TXT))
 DOC_MAN7=$(patsubst %.txt,%.7,$(MAN7_TXT))
 
 prefix?=$(HOME)
-bin=$(prefix)/bin
-mandir=$(prefix)/man
-man1=$(mandir)/man1
-man7=$(mandir)/man7
+bindir?=$(prefix)/bin
+mandir?=$(prefix)/man
+man1dir=$(mandir)/man1
+man7dir=$(mandir)/man7
 # DESTDIR=
 
 INSTALL?=install
@@ -46,15 +46,16 @@ all: html man
 
 html: $(DOC_HTML)
 
+$(DOC_HTML) $(DOC_MAN1) $(DOC_MAN7): asciidoc.conf
 
 man: man1 man7
 man1: $(DOC_MAN1)
 man7: $(DOC_MAN7)
 
 install: man
-	$(INSTALL) -d -m755 $(DESTDIR)$(man1) $(DESTDIR)$(man7)
-	$(INSTALL) $(DOC_MAN1) $(DESTDIR)$(man1)
-	$(INSTALL) $(DOC_MAN7) $(DESTDIR)$(man7)
+	$(INSTALL) -d -m755 $(DESTDIR)$(man1dir) $(DESTDIR)$(man7dir)
+	$(INSTALL) $(DOC_MAN1) $(DESTDIR)$(man1dir)
+	$(INSTALL) $(DOC_MAN7) $(DESTDIR)$(man7dir)
 
 
 #
diff --git a/Documentation/asciidoc.conf b/Documentation/asciidoc.conf
index 7ce71510de..8196d787ab 100644
--- a/Documentation/asciidoc.conf
+++ b/Documentation/asciidoc.conf
@@ -9,6 +9,8 @@
 
 [attributes]
 caret=^
+startsb=[
+endsb=]
 
 ifdef::backend-docbook[]
 [gitlink-inlinemacro]
diff --git a/Documentation/config.txt b/Documentation/config.txt
index 0b434c1f19..465eb13e76 100644
--- a/Documentation/config.txt
+++ b/Documentation/config.txt
@@ -97,6 +97,12 @@ core.compression::
 	compression, and 1..9 are various speed/size tradeoffs, 9 being
 	slowest.
 
+core.legacyheaders::
+	A boolean which enables the legacy object header format in case
+	you want to interoperate with old clients accessing the object
+	database directly (where the "http://" and "rsync://" protocols
+	count as direct access).
+
 alias.*::
 	Command aliases for the gitlink:git[1] command wrapper - e.g.
 	after defining "alias.last = cat-file commit HEAD", the invocation
@@ -193,6 +199,10 @@ merge.summary::
 	Whether to include summaries of merged commits in newly created
 	merge commit messages. False by default.
 
+pack.window::
+	The size of the window used by gitlink:git-pack-objects[1] when no
+	window size is given on the command line. Defaults to 10.
+
 pull.octopus::
 	The default merge strategy to use when pulling multiple branches
 	at once.
@@ -208,6 +218,17 @@ showbranch.default::
 	The default set of branches for gitlink:git-show-branch[1].
 	See gitlink:git-show-branch[1].
 
+tar.umask::
+	By default, git-link:git-tar-tree[1] sets file and directories modes
+	to 0666 or 0777. While this is both useful and acceptable for projects
+	such as the Linux Kernel, it might be excessive for other projects.
+	With this variable, it becomes possible to tell
+	git-link:git-tar-tree[1] to apply a specific umask to the modes above.
+	The special value "user" indicates that the user's current umask will
+	be used. This should be enough for most projects, as it will lead to
+	the same permissions as git-link:git-checkout[1] would use. The default
+	value remains 0, which means world read-write.
+
 user.email::
 	Your email address to be recorded in any newly created commits.
 	Can be overridden by the 'GIT_AUTHOR_EMAIL' and 'GIT_COMMITTER_EMAIL'
diff --git a/Documentation/git-cvsexportcommit.txt b/Documentation/git-cvsexportcommit.txt
index 27ac72d98f..092d0d6730 100644
--- a/Documentation/git-cvsexportcommit.txt
+++ b/Documentation/git-cvsexportcommit.txt
@@ -8,7 +8,7 @@ git-cvsexportcommit - Export a commit to a CVS checkout
 
 SYNOPSIS
 --------
-'git-cvsexportcommit' [-h] [-v] [-c] [-p] [-f] [-m msgprefix] [PARENTCOMMIT] COMMITID
+'git-cvsexportcommit' [-h] [-v] [-c] [-p] [-a] [-f] [-m msgprefix] [PARENTCOMMIT] COMMITID
 
 
 DESCRIPTION
@@ -36,9 +36,13 @@ OPTIONS
 	commit if any hunks fail to apply or there were other problems.
 
 -p::
-	Be pedantic (paranoid) when applying patches. Invokes patch with 
+	Be pedantic (paranoid) when applying patches. Invokes patch with
 	--fuzz=0
 
+-a::
+	Add authorship information. Adds Author line, and Committer (if
+	different from Author) to the message.
+
 -f::
 	Force the merge even if the files are not up to date.
 
diff --git a/Documentation/git-daemon.txt b/Documentation/git-daemon.txt
index 4c357daf6a..0f7d274eab 100644
--- a/Documentation/git-daemon.txt
+++ b/Documentation/git-daemon.txt
@@ -11,7 +11,7 @@ SYNOPSIS
 'git-daemon' [--verbose] [--syslog] [--inetd | --port=n] [--export-all]
              [--timeout=n] [--init-timeout=n] [--strict-paths]
              [--base-path=path] [--user-path | --user-path=path]
-	     [directory...]
+	     [--reuseaddr] [--detach] [--pid-file=file] [directory...]
 
 DESCRIPTION
 -----------
@@ -82,6 +82,17 @@ OPTIONS
 --verbose::
 	Log details about the incoming connections and requested files.
 
+--reuseaddr::
+	Use SO_REUSEADDR when binding the listening socket.
+	This allows the server to restart without waiting for
+	old connections to time out.
+
+--detach::
+	Detach from the shell. Implies --syslog.
+
+--pid-file=file::
+	Save the process id in 'file'.
+
 <directory>::
 	A directory to add to the whitelist of allowed directories. Unless
 	--strict-paths is specified this will also include subdirectories
diff --git a/Documentation/git-format-patch.txt b/Documentation/git-format-patch.txt
index 4ca0014dac..67425dc035 100644
--- a/Documentation/git-format-patch.txt
+++ b/Documentation/git-format-patch.txt
@@ -9,8 +9,9 @@ git-format-patch - Prepare patches for e-mail submission
 SYNOPSIS
 --------
 [verse]
-'git-format-patch' [-n | -k] [-o <dir> | --stdout] [--attach]
+'git-format-patch' [-n | -k] [-o <dir> | --stdout] [--attach] [--thread]
 	           [-s | --signoff] [--diff-options] [--start-number <n>]
+		   [--in-reply-to=Message-Id]
 		   <since>[..<until>]
 
 DESCRIPTION
@@ -35,6 +36,10 @@ they are created in the current working directory.
 If -n is specified, instead of "[PATCH] Subject", the first line
 is formatted as "[PATCH n/m] Subject".
 
+If given --thread, git-format-patch will generate In-Reply-To and
+References headers to make the second and subsequent patch mails appear
+as replies to the first mail; this also generates a Message-Id header to
+reference.
 
 OPTIONS
 -------
@@ -63,6 +68,15 @@ OPTIONS
 --attach::
 	Create attachments instead of inlining patches.
 
+--thread::
+	Add In-Reply-To and References headers to make the second and
+	subsequent mails appear as replies to the first.  Also generates
+	the Message-Id header to reference.
+
+--in-reply-to=Message-Id::
+	Make the first mail (or all the mails with --no-thread) appear as a
+	reply to the given Message-Id, which avoids breaking threads to
+	provide a new patch series.
 
 CONFIGURATION
 -------------
diff --git a/Documentation/git-http-fetch.txt b/Documentation/git-http-fetch.txt
index bc1a132891..3d508094af 100644
--- a/Documentation/git-http-fetch.txt
+++ b/Documentation/git-http-fetch.txt
@@ -8,7 +8,7 @@ git-http-fetch - downloads a remote git repository via HTTP
 
 SYNOPSIS
 --------
-'git-http-fetch' [-c] [-t] [-a] [-d] [-v] [-w filename] [--recover] <commit> <url>
+'git-http-fetch' [-c] [-t] [-a] [-d] [-v] [-w filename] [--recover] [--stdin] <commit> <url>
 
 DESCRIPTION
 -----------
@@ -33,6 +33,12 @@ commit-id::
         Writes the commit-id into the filename under $GIT_DIR/refs/<filename> on
         the local end after the transfer is complete.
 
+--stdin::
+	Instead of a commit id on the commandline (which is not expected in this
+	case), 'git-http-fetch' expects lines on stdin in the format
+
+		<commit-id>['\t'<filename-as-in--w>]
+
 Author
 ------
 Written by Linus Torvalds <torvalds@osdl.org>
diff --git a/Documentation/git-local-fetch.txt b/Documentation/git-local-fetch.txt
index 87abec1c4e..2fbdfe086a 100644
--- a/Documentation/git-local-fetch.txt
+++ b/Documentation/git-local-fetch.txt
@@ -29,6 +29,12 @@ OPTIONS
         Writes the commit-id into the filename under $GIT_DIR/refs/<filename> on
         the local end after the transfer is complete.
 
+--stdin::
+	Instead of a commit id on the commandline (which is not expected in this
+	case), 'git-local-fetch' expects lines on stdin in the format
+
+		<commit-id>['\t'<filename-as-in--w>]
+
 Author
 ------
 Written by Junio C Hamano <junkio@cox.net>
diff --git a/Documentation/git-tar-tree.txt b/Documentation/git-tar-tree.txt
index f2675c4193..1e1c7fa856 100644
--- a/Documentation/git-tar-tree.txt
+++ b/Documentation/git-tar-tree.txt
@@ -37,7 +37,20 @@ OPTIONS
 	Instead of making a tar archive from local repository,
 	retrieve a tar archive from a remote repository.
 
-Examples
+CONFIGURATION
+-------------
+By default, file and directories modes are set to 0666 or 0777. It is
+possible to change this by setting the "umask" variable in the
+repository configuration as follows :
+
+[tar]
+        umask = 002	;# group friendly
+
+The special umask value "user" indicates that the user's current umask
+will be used instead. The default value remains 0, which means world
+readable/writable files and directories.
+
+EXAMPLES
 --------
 git tar-tree HEAD junk | (cd /var/tmp/ && tar xf -)::
 
@@ -58,6 +71,11 @@ git tar-tree --remote=example.com:git.git v1.4.0 >git-1.4.0.tar::
 
 	Get a tarball v1.4.0 from example.com.
 
+git tar-tree HEAD:Documentation/ git-docs > git-1.4.0-docs.tar::
+
+	Put everything in the current head's Documentation/ directory
+	into 'git-1.4.0-docs.tar', with the prefix 'git-docs/'.
+
 Author
 ------
 Written by Rene Scharfe.
diff --git a/Documentation/git.txt b/Documentation/git.txt
index ce3058182f..7310a2b8b8 100644
--- a/Documentation/git.txt
+++ b/Documentation/git.txt
@@ -8,7 +8,8 @@ git - the stupid content tracker
 
 SYNOPSIS
 --------
-'git' [--version] [--exec-path[=GIT_EXEC_PATH]] [--help] COMMAND [ARGS]
+'git' [--version] [--exec-path[=GIT_EXEC_PATH]] [-p|--paginate]
+	[--bare] [--git-dir=GIT_DIR] [--help] COMMAND [ARGS]
 
 DESCRIPTION
 -----------
@@ -41,6 +42,15 @@ OPTIONS
 	environment variable. If no path is given 'git' will print
 	the current setting and then exit.
 
+-p|--paginate::
+	Pipe all output into 'less' (or if set, $PAGER).
+
+--git-dir=<path>::
+	Set the path to the repository. This can also be controlled by
+	setting the GIT_DIR environment variable.
+
+--bare::
+	Same as --git-dir=`pwd`.
 
 FURTHER DOCUMENTATION
 ---------------------
diff --git a/Documentation/urls.txt b/Documentation/urls.txt
index 93378d2378..26ecba53fb 100644
--- a/Documentation/urls.txt
+++ b/Documentation/urls.txt
@@ -10,20 +10,21 @@ to name the remote repository:
 - https://host.xz/path/to/repo.git/
 - git://host.xz/path/to/repo.git/
 - git://host.xz/~user/path/to/repo.git/
-- ssh://+++[user@+++]host.xz/path/to/repo.git/
-- ssh://+++[user@+++]host.xz/~user/path/to/repo.git/
-- ssh://+++[user@+++]host.xz/~/path/to/repo.git
+- ssh://{startsb}user@{endsb}host.xz/path/to/repo.git/
+- ssh://{startsb}user@{endsb}host.xz/~user/path/to/repo.git/
+- ssh://{startsb}user@{endsb}host.xz/~/path/to/repo.git
 ===============================================================
 
-SSH Is the default transport protocol and also supports an
-scp-like syntax.  Both syntaxes support username expansion,
+SSH is the default transport protocol.  You can optionally specify
+which user to log-in as, and an alternate, scp-like syntax is also
+supported.  Both syntaxes support username expansion,
 as does the native git protocol. The following three are
 identical to the last three above, respectively:
 
 ===============================================================
-- host.xz:/path/to/repo.git/
-- host.xz:~user/path/to/repo.git/
-- host.xz:path/to/repo.git
+- {startsb}user@{endsb}host.xz:/path/to/repo.git/
+- {startsb}user@{endsb}host.xz:~user/path/to/repo.git/
+- {startsb}user@{endsb}host.xz:path/to/repo.git
 ===============================================================
 
 To sync with a local directory, use:
diff --git a/INSTALL b/INSTALL
index 7da2c89829..ba9778cd4d 100644
--- a/INSTALL
+++ b/INSTALL
@@ -13,6 +13,15 @@ that uses $prefix, the built results have some paths encoded,
 which are derived from $prefix, so "make all; make prefix=/usr
 install" would not work.
 
+Alternatively you can use autoconf generated ./configure script to
+set up install paths (via config.mak.autogen), so you can write instead
+
+	$ autoconf ;# as yourself if ./configure doesn't exist yet
+	$ ./configure --prefix=/usr ;# as yourself
+	$ make all doc ;# as yourself
+	# make install install-doc ;# as root
+
+
 Issues of note:
 
  - git normally installs a helper script wrapper called "git", which
diff --git a/Makefile b/Makefile
index 12ffd45ca9..b7a095f0dd 100644
--- a/Makefile
+++ b/Makefile
@@ -37,6 +37,18 @@ all:
 # tests.  These tests take up a significant amount of the total test time
 # but are not needed unless you plan to talk to SVN repos.
 #
+# Define NO_FINK if you are building on Darwin/Mac OS X, have Fink
+# installed in /sw, but don't want GIT to link against any libraries
+# installed there.  If defined you may specify your own (or Fink's)
+# include directories and library directories by defining CFLAGS
+# and LDFLAGS appropriately.
+#
+# Define NO_DARWIN_PORTS if you are building on Darwin/Mac OS X,
+# have DarwinPorts installed in /opt/local, but don't want GIT to
+# link against any libraries installed there.  If defined you may
+# specify your own (or DarwinPort's) include directories and
+# library directories by defining CFLAGS and LDFLAGS appropriately.
+#
 # Define PPC_SHA1 environment variable when running make to make use of
 # a bundled SHA1 routine optimized for PowerPC.
 #
@@ -104,6 +116,8 @@ template_dir = $(prefix)/share/git-core/templates/
 GIT_PYTHON_DIR = $(prefix)/share/git-core/python
 # DESTDIR=
 
+export prefix bindir gitexecdir template_dir GIT_PYTHON_DIR
+
 CC = gcc
 AR = ar
 TAR = tar
@@ -137,7 +151,7 @@ SCRIPT_PERL = \
 	git-archimport.perl git-cvsimport.perl git-relink.perl \
 	git-shortlog.perl git-rerere.perl \
 	git-annotate.perl git-cvsserver.perl \
-	git-svnimport.perl git-mv.perl git-cvsexportcommit.perl \
+	git-svnimport.perl git-cvsexportcommit.perl \
 	git-send-email.perl git-svn.perl
 
 SCRIPT_PYTHON = \
@@ -179,7 +193,7 @@ BUILT_INS = git-log$X git-whatchanged$X git-show$X git-update-ref$X \
 	git-read-tree$X git-commit-tree$X git-write-tree$X \
 	git-apply$X git-show-branch$X git-diff-files$X git-update-index$X \
 	git-diff-index$X git-diff-stages$X git-diff-tree$X git-cat-file$X \
-	git-fmt-merge-msg$X git-prune$X
+	git-fmt-merge-msg$X git-prune$X git-mv$X
 
 # what 'all' will build and 'install' will install, in gitexecdir
 ALL_PROGRAMS = $(PROGRAMS) $(SIMPLE_PROGRAMS) $(SCRIPTS)
@@ -208,7 +222,7 @@ LIB_H = \
 	blob.h cache.h commit.h csum-file.h delta.h \
 	diff.h object.h pack.h pkt-line.h quote.h refs.h \
 	run-command.h strbuf.h tag.h tree.h git-compat-util.h revision.h \
-	tree-walk.h log-tree.h dir.h
+	tree-walk.h log-tree.h dir.h path-list.h unpack-trees.h
 
 DIFF_OBJS = \
 	diff.o diff-lib.o diffcore-break.o diffcore-order.o \
@@ -223,7 +237,7 @@ LIB_OBJS = \
 	server-info.o setup.o sha1_file.o sha1_name.o strbuf.o \
 	tag.o tree.o usage.o config.o environment.o ctype.o copy.o \
 	fetch-clone.o revision.o pager.o tree-walk.o xdiff-interface.o \
-	alloc.o merge-file.o $(DIFF_OBJS)
+	alloc.o merge-file.o path-list.o unpack-trees.o $(DIFF_OBJS)
 
 BUILTIN_OBJS = \
 	builtin-log.o builtin-help.o builtin-count.o builtin-diff.o builtin-push.o \
@@ -235,7 +249,8 @@ BUILTIN_OBJS = \
 	builtin-apply.o builtin-show-branch.o builtin-diff-files.o \
 	builtin-diff-index.o builtin-diff-stages.o builtin-diff-tree.o \
 	builtin-cat-file.o builtin-mailsplit.o builtin-stripspace.o \
-	builtin-update-ref.o builtin-fmt-merge-msg.o builtin-prune.o
+	builtin-update-ref.o builtin-fmt-merge-msg.o builtin-prune.o \
+	builtin-mv.o
 
 GITLIBS = $(LIB_FILE) $(XDIFF_LIB)
 LIBS = $(GITLIBS) -lz
@@ -251,19 +266,24 @@ LIBS = $(GITLIBS) -lz
 ifeq ($(uname_S),Linux)
 	NO_STRLCPY = YesPlease
 endif
+ifeq ($(uname_S),GNU/kFreeBSD)
+	NO_STRLCPY = YesPlease
+endif
 ifeq ($(uname_S),Darwin)
 	NEEDS_SSL_WITH_CRYPTO = YesPlease
 	NEEDS_LIBICONV = YesPlease
 	NO_STRLCPY = YesPlease
-	## fink
-	ifeq ($(shell test -d /sw/lib && echo y),y)
-		ALL_CFLAGS += -I/sw/include
-		ALL_LDFLAGS += -L/sw/lib
+	ifndef NO_FINK
+		ifeq ($(shell test -d /sw/lib && echo y),y)
+			ALL_CFLAGS += -I/sw/include
+			ALL_LDFLAGS += -L/sw/lib
+		endif
 	endif
-	## darwinports
-	ifeq ($(shell test -d /opt/local/lib && echo y),y)
-		ALL_CFLAGS += -I/opt/local/include
-		ALL_LDFLAGS += -L/opt/local/lib
+	ifndef NO_DARWIN_PORTS
+		ifeq ($(shell test -d /opt/local/lib && echo y),y)
+			ALL_CFLAGS += -I/opt/local/include
+			ALL_LDFLAGS += -L/opt/local/lib
+		endif
 	endif
 endif
 ifeq ($(uname_S),SunOS)
@@ -337,6 +357,7 @@ ifneq (,$(findstring arm,$(uname_M)))
 	ARM_SHA1 = YesPlease
 endif
 
+-include config.mak.autogen
 -include config.mak
 
 ifdef WITH_OWN_SUBPROCESS_PY
@@ -562,7 +583,7 @@ git-instaweb: git-instaweb.sh gitweb/gitweb.cgi gitweb/gitweb.css
 	    -e '/@@GITWEB_CGI@@/d' \
 	    -e '/@@GITWEB_CSS@@/r gitweb/gitweb.css' \
 	    -e '/@@GITWEB_CSS@@/d' \
-	    $@.sh > $@+
+	    $@.sh | sed "s|/usr/bin/git|$(bindir)/git|" > $@+
 	chmod +x $@+
 	mv $@+ $@
 
@@ -599,6 +620,8 @@ $(SIMPLE_PROGRAMS) : git-%$X : %.o
 	$(CC) $(ALL_CFLAGS) -o $@ $(ALL_LDFLAGS) $(filter %.o,$^) \
 		$(LIB_FILE) $(SIMPLE_LIB)
 
+ssh-pull.o: ssh-fetch.c
+ssh-push.o: ssh-upload.c
 git-local-fetch$X: fetch.o
 git-ssh-fetch$X: rsh.o fetch.o
 git-ssh-upload$X: rsh.o
@@ -745,8 +768,8 @@ dist-doc:
 	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 \
+		man1dir=../.doc-tmp-dir/man1 \
+		man7dir=../.doc-tmp-dir/man7 \
 		install
 	cd .doc-tmp-dir && $(TAR) cf ../$(manpages).tar .
 	gzip -n -9 -f $(manpages).tar
@@ -759,6 +782,8 @@ 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 autom4te.cache
+	rm -f config.log config.mak.autogen configure config.status config.cache
 	rm -rf $(GIT_TARNAME) .doc-tmp-dir
 	rm -f $(GIT_TARNAME).tar.gz git-core_$(GIT_VERSION)-*.tar.gz
 	rm -f $(htmldocs).tar.gz $(manpages).tar.gz
diff --git a/blame.c b/blame.c
index b04b8f58aa..76712b5962 100644
--- a/blame.c
+++ b/blame.c
@@ -834,7 +834,7 @@ int main(int argc, const char **argv)
 	}
 
 
-	init_revisions(&rev);
+	init_revisions(&rev, setup_git_directory());
 	rev.remove_empty_trees = 1;
 	rev.topo_order = 1;
 	rev.prune_fn = simplify_commit;
diff --git a/builtin-add.c b/builtin-add.c
index 2d25698173..f548b8007d 100644
--- a/builtin-add.c
+++ b/builtin-add.c
@@ -21,8 +21,7 @@ static void prune_directory(struct dir_struct *dir, const char **pathspec, int p
 
 	for (specs = 0; pathspec[specs];  specs++)
 		/* nothing */;
-	seen = xmalloc(specs);
-	memset(seen, 0, specs);
+	seen = xcalloc(specs, 1);
 
 	src = dst = dir->entries;
 	i = dir->nr;
@@ -83,52 +82,12 @@ static void fill_directory(struct dir_struct *dir, const char **pathspec)
 		prune_directory(dir, pathspec, baselen);
 }
 
-static int add_file_to_index(const char *path, int verbose)
-{
-	int size, namelen;
-	struct stat st;
-	struct cache_entry *ce;
-
-	if (lstat(path, &st))
-		die("%s: unable to stat (%s)", path, strerror(errno));
-
-	if (!S_ISREG(st.st_mode) && !S_ISLNK(st.st_mode))
-		die("%s: can only add regular files or symbolic links", path);
-
-	namelen = strlen(path);
-	size = cache_entry_size(namelen);
-	ce = xcalloc(1, size);
-	memcpy(ce->name, path, namelen);
-	ce->ce_flags = htons(namelen);
-	fill_stat_cache_info(ce, &st);
-
-	ce->ce_mode = create_ce_mode(st.st_mode);
-	if (!trust_executable_bit) {
-		/* If there is an existing entry, pick the mode bits
-		 * from it.
-		 */
-		int pos = cache_name_pos(path, namelen);
-		if (pos >= 0)
-			ce->ce_mode = active_cache[pos]->ce_mode;
-	}
-
-	if (index_path(ce->sha1, path, &st, 1))
-		die("unable to index file %s", path);
-	if (add_cache_entry(ce, ADD_CACHE_OK_TO_ADD))
-		die("unable to add %s to index",path);
-	if (verbose)
-		printf("add '%s'\n", path);
-	cache_tree_invalidate_path(active_cache_tree, path);
-	return 0;
-}
-
 static struct lock_file lock_file;
 
-int cmd_add(int argc, const char **argv, char **envp)
+int cmd_add(int argc, const char **argv, const char *prefix)
 {
 	int i, newfd;
 	int verbose = 0, show_only = 0;
-	const char *prefix = setup_git_directory();
 	const char **pathspec;
 	struct dir_struct dir;
 
@@ -160,7 +119,6 @@ int cmd_add(int argc, const char **argv, char **envp)
 		}
 		die(builtin_add_usage);
 	}
-	git_config(git_default_config);
 	pathspec = get_pathspec(prefix, argv + i);
 
 	fill_directory(&dir, pathspec);
diff --git a/builtin-apply.c b/builtin-apply.c
index c903146bb6..f8c6763c74 100644
--- a/builtin-apply.c
+++ b/builtin-apply.c
@@ -120,7 +120,7 @@ struct fragment {
 struct patch {
 	char *new_name, *old_name, *def_name;
 	unsigned int old_mode, new_mode;
-	int is_rename, is_copy, is_new, is_delete, is_binary;
+	int is_rename, is_copy, is_new, is_delete, is_binary, is_reverse;
 #define BINARY_DELTA_DEFLATED 1
 #define BINARY_LITERAL_DEFLATED 2
 	unsigned long deflate_origlen;
@@ -1119,6 +1119,34 @@ static int parse_chunk(char *buffer, unsigned long size, struct patch *patch)
 	return offset + hdrsize + patchsize;
 }
 
+#define swap(a,b) myswap((a),(b),sizeof(a))
+
+#define myswap(a, b, size) do {		\
+	unsigned char mytmp[size];	\
+	memcpy(mytmp, &a, size);		\
+	memcpy(&a, &b, size);		\
+	memcpy(&b, mytmp, size);		\
+} while (0)
+
+static void reverse_patches(struct patch *p)
+{
+	for (; p; p = p->next) {
+		struct fragment *frag = p->fragments;
+
+		swap(p->new_name, p->old_name);
+		swap(p->new_mode, p->old_mode);
+		swap(p->is_new, p->is_delete);
+		swap(p->lines_added, p->lines_deleted);
+		swap(p->old_sha1_prefix, p->new_sha1_prefix);
+
+		for (; frag; frag = frag->next) {
+			swap(frag->newpos, frag->oldpos);
+			swap(frag->newlines, frag->oldlines);
+		}
+		p->is_reverse = !p->is_reverse;
+	}
+}
+
 static const char pluses[] = "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++";
 static const char minuses[]= "----------------------------------------------------------------------";
 
@@ -1336,7 +1364,7 @@ static int apply_line(char *output, const char *patch, int plen)
 }
 
 static int apply_one_fragment(struct buffer_desc *desc, struct fragment *frag,
-	int inaccurate_eof)
+	int reverse, int inaccurate_eof)
 {
 	int match_beginning, match_end;
 	char *buf = desc->buffer;
@@ -1350,6 +1378,7 @@ static int apply_one_fragment(struct buffer_desc *desc, struct fragment *frag,
 	int pos, lines;
 
 	while (size > 0) {
+		char first;
 		int len = linelen(patch, size);
 		int plen;
 
@@ -1366,16 +1395,23 @@ static int apply_one_fragment(struct buffer_desc *desc, struct fragment *frag,
 		plen = len-1;
 		if (len < size && patch[len] == '\\')
 			plen--;
-		switch (*patch) {
+		first = *patch;
+		if (reverse) {
+			if (first == '-')
+				first = '+';
+			else if (first == '+')
+				first = '-';
+		}
+		switch (first) {
 		case ' ':
 		case '-':
 			memcpy(old + oldsize, patch + 1, plen);
 			oldsize += plen;
-			if (*patch == '-')
+			if (first == '-')
 				break;
 		/* Fall-through for ' ' */
 		case '+':
-			if (*patch != '+' || !no_add)
+			if (first != '+' || !no_add)
 				newsize += apply_line(new + newsize, patch,
 						      plen);
 			break;
@@ -1499,6 +1535,12 @@ static int apply_binary_fragment(struct buffer_desc *desc, struct patch *patch)
 	void *data;
 	void *result;
 
+	/* Binary patch is irreversible */
+	if (patch->is_reverse)
+		return error("cannot reverse-apply a binary patch to '%s'",
+			     patch->new_name
+			     ? patch->new_name : patch->old_name);
+
 	data = inflate_it(fragment->patch, fragment->size,
 			  patch->deflate_origlen);
 	if (!data)
@@ -1615,7 +1657,8 @@ static int apply_fragments(struct buffer_desc *desc, struct patch *patch)
 		return apply_binary(desc, patch);
 
 	while (frag) {
-		if (apply_one_fragment(desc, frag, patch->inaccurate_eof) < 0)
+		if (apply_one_fragment(desc, frag, patch->is_reverse,
+					patch->inaccurate_eof) < 0)
 			return error("patch failed: %s:%ld",
 				     name, frag->oldpos);
 		frag = frag->next;
@@ -1664,13 +1707,14 @@ static int apply_data(struct patch *patch, struct stat *st, struct cache_entry *
 	return 0;
 }
 
-static int check_patch(struct patch *patch)
+static int check_patch(struct patch *patch, struct patch *prev_patch)
 {
 	struct stat st;
 	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;
+	int ok_if_exists;
 
 	if (old_name) {
 		int changed = 0;
@@ -1728,13 +1772,33 @@ static int check_patch(struct patch *patch)
 				old_name, st_mode, patch->old_mode);
 	}
 
+	if (new_name && prev_patch && prev_patch->is_delete &&
+	    !strcmp(prev_patch->old_name, new_name))
+		/* A type-change diff is always split into a patch to
+		 * delete old, immediately followed by a patch to
+		 * create new (see diff.c::run_diff()); in such a case
+		 * it is Ok that the entry to be deleted by the
+		 * previous patch is still in the working tree and in
+		 * the index.
+		 */
+		ok_if_exists = 1;
+	else
+		ok_if_exists = 0;
+
 	if (new_name && (patch->is_new | patch->is_rename | patch->is_copy)) {
-		if (check_index && cache_name_pos(new_name, strlen(new_name)) >= 0)
+		if (check_index &&
+		    cache_name_pos(new_name, strlen(new_name)) >= 0 &&
+		    !ok_if_exists)
 			return error("%s: already exists in index", new_name);
 		if (!cached) {
-			if (!lstat(new_name, &st))
-				return error("%s: already exists in working directory", new_name);
-			if (errno != ENOENT)
+			struct stat nst;
+			if (!lstat(new_name, &nst)) {
+				if (S_ISDIR(nst.st_mode) || ok_if_exists)
+					; /* ok */
+				else
+					return error("%s: already exists in working directory", new_name);
+			}
+			else if ((errno != ENOENT) && (errno != ENOTDIR))
 				return error("%s: %s", new_name, strerror(errno));
 		}
 		if (!patch->new_mode) {
@@ -1762,10 +1826,13 @@ static int check_patch(struct patch *patch)
 
 static int check_patch_list(struct patch *patch)
 {
+	struct patch *prev_patch = NULL;
 	int error = 0;
 
-	for (;patch ; patch = patch->next)
-		error |= check_patch(patch);
+	for (prev_patch = NULL; patch ; patch = patch->next) {
+		error |= check_patch(patch, prev_patch);
+		prev_patch = patch;
+	}
 	return error;
 }
 
@@ -2010,6 +2077,16 @@ static void create_one_file(char *path, unsigned mode, const char *buf, unsigned
 			return;
 	}
 
+	if (errno == EEXIST || errno == EACCES) {
+		/* We may be trying to create a file where a directory
+		 * used to be.
+		 */
+		struct stat st;
+		errno = 0;
+		if (!lstat(path, &st) && S_ISDIR(st.st_mode) && !rmdir(path))
+			errno = EEXIST;
+	}
+
 	if (errno == EEXIST) {
 		unsigned int nr = getpid();
 
@@ -2044,32 +2121,42 @@ static void create_file(struct patch *patch)
 	cache_tree_invalidate_path(active_cache_tree, path);
 }
 
-static void write_out_one_result(struct patch *patch)
+/* phase zero is to remove, phase one is to create */
+static void write_out_one_result(struct patch *patch, int phase)
 {
 	if (patch->is_delete > 0) {
-		remove_file(patch);
+		if (phase == 0)
+			remove_file(patch);
 		return;
 	}
 	if (patch->is_new > 0 || patch->is_copy) {
-		create_file(patch);
+		if (phase == 1)
+			create_file(patch);
 		return;
 	}
 	/*
 	 * Rename or modification boils down to the same
 	 * thing: remove the old, write the new
 	 */
-	remove_file(patch);
+	if (phase == 0)
+		remove_file(patch);
+	if (phase == 1)
 	create_file(patch);
 }
 
 static void write_out_results(struct patch *list, int skipped_patch)
 {
+	int phase;
+
 	if (!list && !skipped_patch)
 		die("No changes");
 
-	while (list) {
-		write_out_one_result(list);
-		list = list->next;
+	for (phase = 0; phase < 2; phase++) {
+		struct patch *l = list;
+		while (l) {
+			write_out_one_result(l, phase);
+			l = l->next;
+		}
 	}
 }
 
@@ -2098,7 +2185,8 @@ static int use_patch(struct patch *p)
 	return 1;
 }
 
-static int apply_patch(int fd, const char *filename, int inaccurate_eof)
+static int apply_patch(int fd, const char *filename,
+		int reverse, int inaccurate_eof)
 {
 	unsigned long offset, size;
 	char *buffer = read_patch_file(fd, &size);
@@ -2118,6 +2206,8 @@ static int apply_patch(int fd, const char *filename, int inaccurate_eof)
 		nr = parse_chunk(buffer + offset, size, patch);
 		if (nr < 0)
 			break;
+		if (reverse)
+			reverse_patches(patch);
 		if (use_patch(patch)) {
 			patch_stats(patch);
 			*listp = patch;
@@ -2178,10 +2268,11 @@ static int git_apply_config(const char *var, const char *value)
 }
 
 
-int cmd_apply(int argc, const char **argv, char **envp)
+int cmd_apply(int argc, const char **argv, const char *prefix)
 {
 	int i;
 	int read_stdin = 1;
+	int reverse = 0;
 	int inaccurate_eof = 0;
 
 	const char *whitespace_option = NULL;
@@ -2192,7 +2283,7 @@ int cmd_apply(int argc, const char **argv, char **envp)
 		int fd;
 
 		if (!strcmp(arg, "-")) {
-			apply_patch(0, "<stdin>", inaccurate_eof);
+			apply_patch(0, "<stdin>", reverse, inaccurate_eof);
 			read_stdin = 0;
 			continue;
 		}
@@ -2269,6 +2360,10 @@ int cmd_apply(int argc, const char **argv, char **envp)
 			parse_whitespace_option(arg + 13);
 			continue;
 		}
+		if (!strcmp(arg, "-R") || !strcmp(arg, "--reverse")) {
+			reverse = 1;
+			continue;
+		}
 		if (!strcmp(arg, "--inaccurate-eof")) {
 			inaccurate_eof = 1;
 			continue;
@@ -2289,12 +2384,12 @@ int cmd_apply(int argc, const char **argv, char **envp)
 			usage(apply_usage);
 		read_stdin = 0;
 		set_default_whitespace_mode(whitespace_option);
-		apply_patch(fd, arg, inaccurate_eof);
+		apply_patch(fd, arg, reverse, inaccurate_eof);
 		close(fd);
 	}
 	set_default_whitespace_mode(whitespace_option);
 	if (read_stdin)
-		apply_patch(0, "<stdin>", inaccurate_eof);
+		apply_patch(0, "<stdin>", reverse, inaccurate_eof);
 	if (whitespace_error) {
 		if (squelch_whitespace_errors &&
 		    squelch_whitespace_errors < whitespace_error) {
diff --git a/builtin-cat-file.c b/builtin-cat-file.c
index 4d36817e5f..814fb0743f 100644
--- a/builtin-cat-file.c
+++ b/builtin-cat-file.c
@@ -94,7 +94,7 @@ static int pprint_tag(const unsigned char *sha1, const char *buf, unsigned long
 	return 0;
 }
 
-int cmd_cat_file(int argc, const char **argv, char **envp)
+int cmd_cat_file(int argc, const char **argv, const char *prefix)
 {
 	unsigned char sha1[20];
 	char type[20];
@@ -102,7 +102,6 @@ int cmd_cat_file(int argc, const char **argv, char **envp)
 	unsigned long size;
 	int opt;
 
-	setup_git_directory();
 	git_config(git_default_config);
 	if (argc != 3)
 		usage("git-cat-file [-t|-s|-e|-p|<type>] <sha1>");
diff --git a/builtin-check-ref-format.c b/builtin-check-ref-format.c
index 4a23936aff..701de439ae 100644
--- a/builtin-check-ref-format.c
+++ b/builtin-check-ref-format.c
@@ -6,7 +6,7 @@
 #include "refs.h"
 #include "builtin.h"
 
-int cmd_check_ref_format(int argc, const char **argv, char **envp)
+int cmd_check_ref_format(int argc, const char **argv, const char *prefix)
 {
 	if (argc != 2)
 		usage("git check-ref-format refname");
diff --git a/builtin-commit-tree.c b/builtin-commit-tree.c
index ec082bf754..9c98796671 100644
--- a/builtin-commit-tree.c
+++ b/builtin-commit-tree.c
@@ -77,7 +77,7 @@ static int new_parent(int idx)
 	return 1;
 }
 
-int cmd_commit_tree(int argc, const char **argv, char **envp)
+int cmd_commit_tree(int argc, const char **argv, const char *prefix)
 {
 	int i;
 	int parents = 0;
@@ -88,8 +88,6 @@ int cmd_commit_tree(int argc, const char **argv, char **envp)
 	unsigned int size;
 
 	setup_ident();
-	setup_git_directory();
-
 	git_config(git_default_config);
 
 	if (argc < 2)
diff --git a/builtin-count.c b/builtin-count.c
index 5ee72df247..1d3729aa99 100644
--- a/builtin-count.c
+++ b/builtin-count.c
@@ -67,7 +67,7 @@ static void count_objects(DIR *d, char *path, int len, int verbose,
 	}
 }
 
-int cmd_count_objects(int ac, const char **av, char **ep)
+int cmd_count_objects(int ac, const char **av, const char *prefix)
 {
 	int i;
 	int verbose = 0;
diff --git a/builtin-diff-files.c b/builtin-diff-files.c
index 81ac2fe64a..ac13db70ff 100644
--- a/builtin-diff-files.c
+++ b/builtin-diff-files.c
@@ -13,13 +13,13 @@ static const char diff_files_usage[] =
 "git-diff-files [-q] [-0/-1/2/3 |-c|--cc] [<common diff options>] [<path>...]"
 COMMON_DIFF_OPTIONS_HELP;
 
-int cmd_diff_files(int argc, const char **argv, char **envp)
+int cmd_diff_files(int argc, const char **argv, const char *prefix)
 {
 	struct rev_info rev;
 	int silent = 0;
 
+	init_revisions(&rev, prefix);
 	git_config(git_default_config); /* no "diff" UI options */
-	init_revisions(&rev);
 	rev.abbrev = 0;
 
 	argc = setup_revisions(argc, argv, &rev, NULL);
diff --git a/builtin-diff-index.c b/builtin-diff-index.c
index a1fa1b85cf..95a3db156b 100644
--- a/builtin-diff-index.c
+++ b/builtin-diff-index.c
@@ -9,14 +9,14 @@ static const char diff_cache_usage[] =
 "[<common diff options>] <tree-ish> [<path>...]"
 COMMON_DIFF_OPTIONS_HELP;
 
-int cmd_diff_index(int argc, const char **argv, char **envp)
+int cmd_diff_index(int argc, const char **argv, const char *prefix)
 {
 	struct rev_info rev;
 	int cached = 0;
 	int i;
 
+	init_revisions(&rev, prefix);
 	git_config(git_default_config); /* no "diff" UI options */
-	init_revisions(&rev);
 	rev.abbrev = 0;
 
 	argc = setup_revisions(argc, argv, &rev, NULL);
diff --git a/builtin-diff-stages.c b/builtin-diff-stages.c
index 9c62702941..5960e08997 100644
--- a/builtin-diff-stages.c
+++ b/builtin-diff-stages.c
@@ -55,10 +55,9 @@ static void diff_stages(int stage1, int stage2, const char **pathspec)
 	}
 }
 
-int cmd_diff_stages(int ac, const char **av, char **envp)
+int cmd_diff_stages(int ac, const char **av, const char *prefix)
 {
 	int stage1, stage2;
-	const char *prefix = setup_git_directory();
 	const char **pathspec = NULL;
 
 	git_config(git_default_config); /* no "diff" UI options */
diff --git a/builtin-diff-tree.c b/builtin-diff-tree.c
index b610668594..24cb2d7f84 100644
--- a/builtin-diff-tree.c
+++ b/builtin-diff-tree.c
@@ -59,7 +59,7 @@ static const char diff_tree_usage[] =
 "  --root        include the initial commit as diff against /dev/null\n"
 COMMON_DIFF_OPTIONS_HELP;
 
-int cmd_diff_tree(int argc, const char **argv, char **envp)
+int cmd_diff_tree(int argc, const char **argv, const char *prefix)
 {
 	int nr_sha1;
 	char line[1000];
@@ -67,9 +67,9 @@ int cmd_diff_tree(int argc, const char **argv, char **envp)
 	static struct rev_info *opt = &log_tree_opt;
 	int read_stdin = 0;
 
+	init_revisions(opt, prefix);
 	git_config(git_default_config); /* no "diff" UI options */
 	nr_sha1 = 0;
-	init_revisions(opt);
 	opt->abbrev = 0;
 	opt->diff = 1;
 	argc = setup_revisions(argc, argv, opt, NULL);
diff --git a/builtin-diff.c b/builtin-diff.c
index cb38f44561..48d2fd03b7 100644
--- a/builtin-diff.c
+++ b/builtin-diff.c
@@ -221,7 +221,7 @@ void add_head(struct rev_info *revs)
 	add_pending_object(revs, obj, "HEAD");
 }
 
-int cmd_diff(int argc, const char **argv, char **envp)
+int cmd_diff(int argc, const char **argv, const char *prefix)
 {
 	int i;
 	struct rev_info rev;
@@ -251,7 +251,7 @@ int cmd_diff(int argc, const char **argv, char **envp)
 	 */
 
 	git_config(git_diff_ui_config);
-	init_revisions(&rev);
+	init_revisions(&rev, prefix);
 
 	argc = setup_revisions(argc, argv, &rev, NULL);
 	if (!rev.diffopt.output_format) {
@@ -346,7 +346,15 @@ int cmd_diff(int argc, const char **argv, char **envp)
 		return builtin_diff_index(&rev, argc, argv);
 	else if (ents == 2)
 		return builtin_diff_tree(&rev, argc, argv, ent);
+	else if ((ents == 3) && (ent[0].item->flags & UNINTERESTING)) {
+		/* diff A...B where there is one sane merge base between
+		 * A and B.  We have ent[0] == merge-base, ent[1] == A,
+		 * and ent[2] == B.  Show diff between the base and B.
+		 */
+		return builtin_diff_tree(&rev, argc, argv, ent);
+	}
 	else
-		return builtin_diff_combined(&rev, argc, argv, ent, ents);
+		return builtin_diff_combined(&rev, argc, argv,
+					     ent, ents);
 	usage(builtin_diff_usage);
 }
diff --git a/builtin-fmt-merge-msg.c b/builtin-fmt-merge-msg.c
index f20b27b8a9..c84224ee84 100644
--- a/builtin-fmt-merge-msg.c
+++ b/builtin-fmt-merge-msg.c
@@ -242,7 +242,7 @@ static void shortlog(const char *name, unsigned char *sha1,
 	free_list(&subjects);
 }
 
-int cmd_fmt_merge_msg(int argc, char **argv, char **envp)
+int cmd_fmt_merge_msg(int argc, char **argv, const char *prefix)
 {
 	int limit = 20, i = 0;
 	char line[1024];
@@ -342,7 +342,7 @@ int cmd_fmt_merge_msg(int argc, char **argv, char **envp)
 		struct rev_info rev;
 
 		head = lookup_commit(head_sha1);
-		init_revisions(&rev);
+		init_revisions(&rev, prefix);
 		rev.commit_format = CMIT_FMT_ONELINE;
 		rev.ignore_merges = 1;
 		rev.limited = 1;
diff --git a/builtin-grep.c b/builtin-grep.c
index a79bac305a..69b7c4862a 100644
--- a/builtin-grep.c
+++ b/builtin-grep.c
@@ -919,14 +919,13 @@ static const char emsg_missing_context_len[] =
 static const char emsg_missing_argument[] =
 "option requires an argument -%s";
 
-int cmd_grep(int argc, const char **argv, char **envp)
+int cmd_grep(int argc, const char **argv, const char *prefix)
 {
 	int hit = 0;
 	int cached = 0;
 	int seen_dashdash = 0;
 	struct grep_opt opt;
 	struct object_array list = { 0, 0, NULL };
-	const char *prefix = setup_git_directory();
 	const char **paths = NULL;
 	int i;
 
diff --git a/builtin-help.c b/builtin-help.c
index 335fe5fedc..bb0b03f1ae 100644
--- a/builtin-help.c
+++ b/builtin-help.c
@@ -221,15 +221,15 @@ static void show_man_page(const char *git_cmd)
 	execlp("man", "man", page, NULL);
 }
 
-int cmd_version(int argc, const char **argv, char **envp)
+int cmd_version(int argc, const char **argv, const char *prefix)
 {
 	printf("git version %s\n", git_version_string);
 	return 0;
 }
 
-int cmd_help(int argc, const char **argv, char **envp)
+int cmd_help(int argc, const char **argv, const char *prefix)
 {
-	const char *help_cmd = argv[1];
+	const char *help_cmd = argc > 1 ? argv[1] : NULL;
 	if (!help_cmd)
 		cmd_usage(0, git_exec_path(), NULL);
 	else if (!strcmp(help_cmd, "--all") || !strcmp(help_cmd, "-a"))
diff --git a/builtin-init-db.c b/builtin-init-db.c
index 7fdd2fa9f9..52473edf56 100644
--- a/builtin-init-db.c
+++ b/builtin-init-db.c
@@ -250,7 +250,7 @@ static const char init_db_usage[] =
  * 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)
+int cmd_init_db(int argc, const char **argv, const char *prefix)
 {
 	const char *git_dir;
 	const char *sha1_dir;
diff --git a/builtin-log.c b/builtin-log.c
index 7e5cab15c1..82c69d1d05 100644
--- a/builtin-log.c
+++ b/builtin-log.c
@@ -10,11 +10,13 @@
 #include "revision.h"
 #include "log-tree.h"
 #include "builtin.h"
+#include <time.h>
+#include <sys/time.h>
 
 /* this is in builtin-diff.c */
 void add_head(struct rev_info *revs);
 
-static void cmd_log_init(int argc, const char **argv, char **envp,
+static void cmd_log_init(int argc, const char **argv, const char *prefix,
 		      struct rev_info *rev)
 {
 	rev->abbrev = DEFAULT_ABBREV;
@@ -43,27 +45,27 @@ static int cmd_log_walk(struct rev_info *rev)
 	return 0;
 }
 
-int cmd_whatchanged(int argc, const char **argv, char **envp)
+int cmd_whatchanged(int argc, const char **argv, const char *prefix)
 {
 	struct rev_info rev;
 
 	git_config(git_diff_ui_config);
-	init_revisions(&rev);
+	init_revisions(&rev, prefix);
 	rev.diff = 1;
 	rev.diffopt.recursive = 1;
 	rev.simplify_history = 0;
-	cmd_log_init(argc, argv, envp, &rev);
+	cmd_log_init(argc, argv, prefix, &rev);
 	if (!rev.diffopt.output_format)
 		rev.diffopt.output_format = DIFF_FORMAT_RAW;
 	return cmd_log_walk(&rev);
 }
 
-int cmd_show(int argc, const char **argv, char **envp)
+int cmd_show(int argc, const char **argv, const char *prefix)
 {
 	struct rev_info rev;
 
 	git_config(git_diff_ui_config);
-	init_revisions(&rev);
+	init_revisions(&rev, prefix);
 	rev.diff = 1;
 	rev.diffopt.recursive = 1;
 	rev.combine_merges = 1;
@@ -71,18 +73,18 @@ int cmd_show(int argc, const char **argv, char **envp)
 	rev.always_show_header = 1;
 	rev.ignore_merges = 0;
 	rev.no_walk = 1;
-	cmd_log_init(argc, argv, envp, &rev);
+	cmd_log_init(argc, argv, prefix, &rev);
 	return cmd_log_walk(&rev);
 }
 
-int cmd_log(int argc, const char **argv, char **envp)
+int cmd_log(int argc, const char **argv, const char *prefix)
 {
 	struct rev_info rev;
 
 	git_config(git_diff_ui_config);
-	init_revisions(&rev);
+	init_revisions(&rev, prefix);
 	rev.always_show_header = 1;
-	cmd_log_init(argc, argv, envp, &rev);
+	cmd_log_init(argc, argv, prefix, &rev);
 	return cmd_log_walk(&rev);
 }
 
@@ -176,7 +178,7 @@ static int get_patch_id(struct commit *commit, struct diff_options *options,
 	return diff_flush_patch_id(options, sha1);
 }
 
-static void get_patch_ids(struct rev_info *rev, struct diff_options *options)
+static void get_patch_ids(struct rev_info *rev, struct diff_options *options, const char *prefix)
 {
 	struct rev_info check_rev;
 	struct commit *commit;
@@ -201,7 +203,7 @@ static void get_patch_ids(struct rev_info *rev, struct diff_options *options)
 		die("diff_setup_done failed");
 
 	/* given a range a..b get all patch ids for b..a */
-	init_revisions(&check_rev);
+	init_revisions(&check_rev, prefix);
 	o1->flags ^= UNINTERESTING;
 	o2->flags ^= UNINTERESTING;
 	add_pending_object(&check_rev, o1, "o1");
@@ -226,7 +228,19 @@ static void get_patch_ids(struct rev_info *rev, struct diff_options *options)
 	o2->flags = flags2;
 }
 
-int cmd_format_patch(int argc, const char **argv, char **envp)
+static void gen_message_id(char *dest, unsigned int length, char *base)
+{
+	const char *committer = git_committer_info(1);
+	const char *email_start = strrchr(committer, '<');
+	const char *email_end = strrchr(committer, '>');
+	if(!email_start || !email_end || email_start > email_end - 1)
+		die("Could not extract email from committer identity.");
+	snprintf(dest, length, "%s.%lu.git.%.*s", base,
+		 (unsigned long) time(NULL),
+		 (int)(email_end - email_start - 1), email_start + 1);
+}
+
+int cmd_format_patch(int argc, const char **argv, const char *prefix)
 {
 	struct commit *commit;
 	struct commit **list = NULL;
@@ -237,11 +251,15 @@ int cmd_format_patch(int argc, const char **argv, char **envp)
 	int start_number = -1;
 	int keep_subject = 0;
 	int ignore_if_in_upstream = 0;
+	int thread = 0;
+	const char *in_reply_to = NULL;
 	struct diff_options patch_id_opts;
 	char *add_signoff = NULL;
+	char message_id[1024];
+	char ref_message_id[1024];
 
 	git_config(git_format_config);
-	init_revisions(&rev);
+	init_revisions(&rev, prefix);
 	rev.commit_format = CMIT_FMT_EMAIL;
 	rev.verbose_header = 1;
 	rev.diff = 1;
@@ -304,6 +322,16 @@ int cmd_format_patch(int argc, const char **argv, char **envp)
 			rev.mime_boundary = argv[i] + 9;
 		else if (!strcmp(argv[i], "--ignore-if-in-upstream"))
 			ignore_if_in_upstream = 1;
+		else if (!strcmp(argv[i], "--thread"))
+			thread = 1;
+		else if (!strncmp(argv[i], "--in-reply-to=", 14))
+			in_reply_to = argv[i] + 14;
+		else if (!strcmp(argv[i], "--in-reply-to")) {
+			i++;
+			if (i == argc)
+				die("Need a Message-Id for --in-reply-to");
+			in_reply_to = argv[i];
+		}
 		else
 			argv[j++] = argv[i];
 	}
@@ -335,7 +363,7 @@ int cmd_format_patch(int argc, const char **argv, char **envp)
 	}
 
 	if (ignore_if_in_upstream)
-		get_patch_ids(&rev, &patch_id_opts);
+		get_patch_ids(&rev, &patch_id_opts, prefix);
 
 	if (!use_stdout)
 		realstdout = fdopen(dup(1), "w");
@@ -361,10 +389,23 @@ int cmd_format_patch(int argc, const char **argv, char **envp)
 	if (numbered)
 		rev.total = total + start_number - 1;
 	rev.add_signoff = add_signoff;
+	rev.ref_message_id = in_reply_to;
 	while (0 <= --nr) {
 		int shown;
 		commit = list[nr];
 		rev.nr = total - nr + (start_number - 1);
+		/* Make the second and subsequent mails replies to the first */
+		if (thread) {
+			if (nr == (total - 2)) {
+				strncpy(ref_message_id, message_id,
+					sizeof(ref_message_id));
+				ref_message_id[sizeof(ref_message_id)-1]='\0';
+				rev.ref_message_id = ref_message_id;
+			}
+			gen_message_id(message_id, sizeof(message_id),
+				       sha1_to_hex(commit->object.sha1));
+			rev.message_id = message_id;
+		}
 		if (!use_stdout)
 			reopen_stdout(commit, rev.nr, keep_subject);
 		shown = log_tree_commit(&rev, commit);
diff --git a/builtin-ls-files.c b/builtin-ls-files.c
index 8dae9f70e2..79ffe8f423 100644
--- a/builtin-ls-files.c
+++ b/builtin-ls-files.c
@@ -322,14 +322,13 @@ static const char ls_files_usage[] =
 	"[ --exclude-per-directory=<filename> ] [--full-name] [--abbrev] "
 	"[--] [<file>]*";
 
-int cmd_ls_files(int argc, const char **argv, char** envp)
+int cmd_ls_files(int argc, const char **argv, const char *prefix)
 {
 	int i;
 	int exc_given = 0;
 	struct dir_struct dir;
 
 	memset(&dir, 0, sizeof(dir));
-	prefix = setup_git_directory();
 	if (prefix)
 		prefix_offset = strlen(prefix);
 	git_config(git_default_config);
diff --git a/builtin-ls-tree.c b/builtin-ls-tree.c
index b8d0d88ba8..261147fdbe 100644
--- a/builtin-ls-tree.c
+++ b/builtin-ls-tree.c
@@ -18,7 +18,7 @@ static int abbrev = 0;
 static int ls_options = 0;
 static const char **pathspec;
 static int chomp_prefix = 0;
-static const char *prefix;
+static const char *ls_tree_prefix;
 
 static const char ls_tree_usage[] =
 	"git-ls-tree [-d] [-r] [-t] [-z] [--name-only] [--name-status] [--full-name] [--abbrev[=<n>]] <tree-ish> [path...]";
@@ -71,7 +71,7 @@ static int show_tree(const unsigned char *sha1, const char *base, int baselen,
 		return 0;
 
 	if (chomp_prefix &&
-	    (baselen < chomp_prefix || memcmp(prefix, base, chomp_prefix)))
+	    (baselen < chomp_prefix || memcmp(ls_tree_prefix, base, chomp_prefix)))
 		return 0;
 
 	if (!(ls_options & LS_NAME_ONLY))
@@ -85,13 +85,13 @@ static int show_tree(const unsigned char *sha1, const char *base, int baselen,
 	return retval;
 }
 
-int cmd_ls_tree(int argc, const char **argv, char **envp)
+int cmd_ls_tree(int argc, const char **argv, const char *prefix)
 {
 	unsigned char sha1[20];
 	struct tree *tree;
 
-	prefix = setup_git_directory();
 	git_config(git_default_config);
+	ls_tree_prefix = prefix;
 	if (prefix && *prefix)
 		chomp_prefix = strlen(prefix);
 	while (1 < argc && argv[1][0] == '-') {
diff --git a/builtin-mailinfo.c b/builtin-mailinfo.c
index ac53f76f68..24a4fc63b3 100644
--- a/builtin-mailinfo.c
+++ b/builtin-mailinfo.c
@@ -446,7 +446,7 @@ static int read_one_header_line(char *line, int sz, FILE *in)
 			break;
 	}
 	/* Count mbox From headers as headers */
-	if (!ofs && !memcmp(line, "From ", 5))
+	if (!ofs && (!memcmp(line, "From ", 5) || !memcmp(line, ">From ", 6)))
 		ofs = 1;
 	return ofs;
 }
@@ -836,7 +836,7 @@ int mailinfo(FILE *in, FILE *out, int ks, const char *encoding,
 static const char mailinfo_usage[] =
 	"git-mailinfo [-k] [-u | --encoding=<encoding>] msg patch <mail >info";
 
-int cmd_mailinfo(int argc, const char **argv, char **envp)
+int cmd_mailinfo(int argc, const char **argv, const char *prefix)
 {
 	/* NEEDSWORK: might want to do the optional .git/ directory
 	 * discovery
diff --git a/builtin-mailsplit.c b/builtin-mailsplit.c
index e2a0058435..91a699d34d 100644
--- a/builtin-mailsplit.c
+++ b/builtin-mailsplit.c
@@ -138,7 +138,7 @@ out:
 	free(name);
 	return ret;
 }
-int cmd_mailsplit(int argc, const char **argv, char **envp)
+int cmd_mailsplit(int argc, const char **argv, const char *prefix)
 {
 	int nr = 0, nr_prec = 4, ret;
 	int allow_bare = 0;
diff --git a/builtin-mv.c b/builtin-mv.c
new file mode 100644
index 0000000000..62ae937cb1
--- /dev/null
+++ b/builtin-mv.c
@@ -0,0 +1,297 @@
+/*
+ * "git mv" builtin command
+ *
+ * Copyright (C) 2006 Johannes Schindelin
+ */
+#include <fnmatch.h>
+
+#include "cache.h"
+#include "builtin.h"
+#include "dir.h"
+#include "cache-tree.h"
+#include "path-list.h"
+
+static const char builtin_mv_usage[] =
+"git-mv [-n] [-f] (<source> <destination> | [-k] <source>... <destination>)";
+
+static const char **copy_pathspec(const char *prefix, const char **pathspec,
+				  int count, int base_name)
+{
+	const char **result = xmalloc((count + 1) * sizeof(const char *));
+	memcpy(result, pathspec, count * sizeof(const char *));
+	result[count] = NULL;
+	if (base_name) {
+		int i;
+		for (i = 0; i < count; i++) {
+			const char *last_slash = strrchr(result[i], '/');
+			if (last_slash)
+				result[i] = last_slash + 1;
+		}
+	}
+	return get_pathspec(prefix, result);
+}
+
+static void show_list(const char *label, struct path_list *list)
+{
+	if (list->nr > 0) {
+		int i;
+		printf("%s", label);
+		for (i = 0; i < list->nr; i++)
+			printf("%s%s", i > 0 ? ", " : "", list->items[i].path);
+		putchar('\n');
+	}
+}
+
+static const char *add_slash(const char *path)
+{
+	int len = strlen(path);
+	if (path[len - 1] != '/') {
+		char *with_slash = xmalloc(len + 2);
+		memcpy(with_slash, path, len);
+		strcat(with_slash + len, "/");
+		return with_slash;
+	}
+	return path;
+}
+
+static struct lock_file lock_file;
+
+int cmd_mv(int argc, const char **argv, const char *prefix)
+{
+	int i, newfd, count;
+	int verbose = 0, show_only = 0, force = 0, ignore_errors = 0;
+	const char **source, **destination, **dest_path;
+	enum update_mode { BOTH = 0, WORKING_DIRECTORY, INDEX } *modes;
+	struct stat st;
+	struct path_list overwritten = {NULL, 0, 0, 0};
+	struct path_list src_for_dst = {NULL, 0, 0, 0};
+	struct path_list added = {NULL, 0, 0, 0};
+	struct path_list deleted = {NULL, 0, 0, 0};
+	struct path_list changed = {NULL, 0, 0, 0};
+
+	git_config(git_default_config);
+
+	newfd = hold_lock_file_for_update(&lock_file, get_index_file());
+	if (newfd < 0)
+		die("unable to create new index file");
+
+	if (read_cache() < 0)
+		die("index file corrupt");
+
+	for (i = 1; i < argc; i++) {
+		const char *arg = argv[i];
+
+		if (arg[0] != '-')
+			break;
+		if (!strcmp(arg, "--")) {
+			i++;
+			break;
+		}
+		if (!strcmp(arg, "-n")) {
+			show_only = 1;
+			continue;
+		}
+		if (!strcmp(arg, "-f")) {
+			force = 1;
+			continue;
+		}
+		if (!strcmp(arg, "-k")) {
+			ignore_errors = 1;
+			continue;
+		}
+		die(builtin_mv_usage);
+	}
+	count = argc - i - 1;
+	if (count < 1)
+		usage(builtin_mv_usage);
+
+	source = copy_pathspec(prefix, argv + i, count, 0);
+	modes = xcalloc(count, sizeof(enum update_mode));
+	dest_path = copy_pathspec(prefix, argv + argc - 1, 1, 0);
+
+	if (!lstat(dest_path[0], &st) &&
+			S_ISDIR(st.st_mode)) {
+		dest_path[0] = add_slash(dest_path[0]);
+		destination = copy_pathspec(dest_path[0], argv + i, count, 1);
+	} else {
+		if (count != 1)
+			usage(builtin_mv_usage);
+		destination = dest_path;
+	}
+
+	/* Checking */
+	for (i = 0; i < count; i++) {
+		const char *bad = NULL;
+
+		if (show_only)
+			printf("Checking rename of '%s' to '%s'\n",
+				source[i], destination[i]);
+
+		if (lstat(source[i], &st) < 0)
+			bad = "bad source";
+
+		if (S_ISDIR(st.st_mode)) {
+			const char *dir = source[i], *dest_dir = destination[i];
+			int first, last, len = strlen(dir);
+
+			if (lstat(dest_dir, &st) == 0) {
+				bad = "cannot move directory over file";
+				goto next;
+			}
+
+			modes[i] = WORKING_DIRECTORY;
+
+			first = cache_name_pos(source[i], len);
+			if (first >= 0)
+				die ("Huh? %s/ is in index?", dir);
+
+			first = -1 - first;
+			for (last = first; last < active_nr; last++) {
+				const char *path = active_cache[last]->name;
+				if (strncmp(path, dir, len) || path[len] != '/')
+					break;
+			}
+
+			if (last - first < 1)
+				bad = "source directory is empty";
+			else if (!bad) {
+				int j, dst_len = strlen(dest_dir);
+
+				if (last - first > 0) {
+					source = realloc(source,
+							(count + last - first)
+							* sizeof(char *));
+					destination = realloc(destination,
+							(count + last - first)
+							* sizeof(char *));
+					modes = realloc(modes,
+							(count + last - first)
+							* sizeof(enum update_mode));
+				}
+
+				dest_dir = add_slash(dest_dir);
+
+				for (j = 0; j < last - first; j++) {
+					const char *path =
+						active_cache[first + j]->name;
+					source[count + j] = path;
+					destination[count + j] =
+						prefix_path(dest_dir, dst_len,
+							path + len);
+					modes[count + j] = INDEX;
+				}
+				count += last - first;
+			}
+
+			goto next;
+		}
+
+		if (!bad && lstat(destination[i], &st) == 0) {
+			bad = "destination exists";
+			if (force) {
+				/*
+				 * only files can overwrite each other:
+				 * check both source and destination
+				 */
+				if (S_ISREG(st.st_mode)) {
+					fprintf(stderr, "Warning: %s;"
+							" will overwrite!\n",
+							bad);
+					bad = NULL;
+					path_list_insert(destination[i],
+							&overwritten);
+				} else
+					bad = "Cannot overwrite";
+			}
+		}
+
+		if (!bad &&
+		    !strncmp(destination[i], source[i], strlen(source[i])))
+			bad = "can not move directory into itself";
+
+		if (!bad && cache_name_pos(source[i], strlen(source[i])) < 0)
+			bad = "not under version control";
+
+		if (!bad) {
+			if (path_list_has_path(&src_for_dst, destination[i]))
+				bad = "multiple sources for the same target";
+			else
+				path_list_insert(destination[i], &src_for_dst);
+		}
+
+next:
+		if (bad) {
+			if (ignore_errors) {
+				if (--count > 0) {
+					memmove(source + i, source + i + 1,
+						(count - i) * sizeof(char *));
+					memmove(destination + i,
+						destination + i + 1,
+						(count - i) * sizeof(char *));
+				}
+			} else
+				die ("%s, source=%s, destination=%s",
+				     bad, source[i], destination[i]);
+		}
+	}
+
+	for (i = 0; i < count; i++) {
+		if (show_only || verbose)
+			printf("Renaming %s to %s\n",
+			       source[i], destination[i]);
+		if (!show_only && modes[i] != INDEX &&
+		    rename(source[i], destination[i]) < 0 &&
+		    !ignore_errors)
+			die ("renaming %s failed: %s",
+			     source[i], strerror(errno));
+
+		if (modes[i] == WORKING_DIRECTORY)
+			continue;
+
+		if (cache_name_pos(source[i], strlen(source[i])) >= 0) {
+			path_list_insert(source[i], &deleted);
+
+			/* destination can be a directory with 1 file inside */
+			if (path_list_has_path(&overwritten, destination[i]))
+				path_list_insert(destination[i], &changed);
+			else
+				path_list_insert(destination[i], &added);
+		} else
+			path_list_insert(destination[i], &added);
+	}
+
+        if (show_only) {
+		show_list("Changed  : ", &changed);
+		show_list("Adding   : ", &added);
+		show_list("Deleting : ", &deleted);
+	} else {
+		for (i = 0; i < changed.nr; i++) {
+			const char *path = changed.items[i].path;
+			int i = cache_name_pos(path, strlen(path));
+			struct cache_entry *ce = active_cache[i];
+
+			if (i < 0)
+				die ("Huh? Cache entry for %s unknown?", path);
+			refresh_cache_entry(ce, 0);
+		}
+
+		for (i = 0; i < added.nr; i++) {
+			const char *path = added.items[i].path;
+			add_file_to_index(path, verbose);
+		}
+
+		for (i = 0; i < deleted.nr; i++) {
+			const char *path = deleted.items[i].path;
+			remove_file_from_cache(path);
+		}
+
+		if (active_cache_changed) {
+			if (write_cache(newfd, active_cache, active_nr) ||
+			    close(newfd) ||
+			    commit_lock_file(&lock_file))
+				die("Unable to write new index file");
+		}
+	}
+
+	return 0;
+}
diff --git a/builtin-prune.c b/builtin-prune.c
index d196c41f13..6a86eb52ae 100644
--- a/builtin-prune.c
+++ b/builtin-prune.c
@@ -217,7 +217,7 @@ static void add_cache_refs(void)
 		add_cache_tree(active_cache_tree);
 }
 
-int cmd_prune(int argc, const char **argv, char **envp)
+int cmd_prune(int argc, const char **argv, const char *prefix)
 {
 	int i;
 
@@ -234,7 +234,7 @@ int cmd_prune(int argc, const char **argv, char **envp)
 	 * Set up revision parsing, and mark us as being interested
 	 * in all object types, not just commits.
 	 */
-	init_revisions(&revs);
+	init_revisions(&revs, prefix);
 	revs.tag_objects = 1;
 	revs.blob_objects = 1;
 	revs.tree_objects = 1;
diff --git a/builtin-push.c b/builtin-push.c
index 31cbfd7386..a824171066 100644
--- a/builtin-push.c
+++ b/builtin-push.c
@@ -270,7 +270,7 @@ static int do_push(const char *repo)
 	return 0;
 }
 
-int cmd_push(int argc, const char **argv, char **envp)
+int cmd_push(int argc, const char **argv, const char *prefix)
 {
 	int i;
 	const char *repo = "origin";	/* default repository */
diff --git a/builtin-read-tree.c b/builtin-read-tree.c
index 6df5d7c5cb..8869cedea1 100644
--- a/builtin-read-tree.c
+++ b/builtin-read-tree.c
@@ -3,419 +3,17 @@
  *
  * Copyright (C) Linus Torvalds, 2005
  */
-#define DBRT_DEBUG 1
 
 #include "cache.h"
-
 #include "object.h"
 #include "tree.h"
 #include "tree-walk.h"
 #include "cache-tree.h"
-#include <sys/time.h>
-#include <signal.h>
+#include "unpack-trees.h"
 #include "builtin.h"
 
-static int reset = 0;
-static int merge = 0;
-static int update = 0;
-static int index_only = 0;
-static int nontrivial_merge = 0;
-static int trivial_merges_only = 0;
-static int aggressive = 0;
-static int verbose_update = 0;
-static volatile int progress_update = 0;
-static const char *prefix = NULL;
-
-static int head_idx = -1;
-static int merge_size = 0;
-
 static struct object_list *trees = NULL;
 
-static struct cache_entry df_conflict_entry;
-
-struct tree_entry_list {
-	struct tree_entry_list *next;
-	unsigned directory : 1;
-	unsigned executable : 1;
-	unsigned symlink : 1;
-	unsigned int mode;
-	const char *name;
-	const unsigned char *sha1;
-};
-
-static struct tree_entry_list df_conflict_list;
-
-typedef int (*merge_fn_t)(struct cache_entry **src);
-
-static struct tree_entry_list *create_tree_entry_list(struct tree *tree)
-{
-	struct tree_desc desc;
-	struct name_entry one;
-	struct tree_entry_list *ret = NULL;
-	struct tree_entry_list **list_p = &ret;
-
-	desc.buf = tree->buffer;
-	desc.size = tree->size;
-
-	while (tree_entry(&desc, &one)) {
-		struct tree_entry_list *entry;
-
-		entry = xmalloc(sizeof(struct tree_entry_list));
-		entry->name = one.path;
-		entry->sha1 = one.sha1;
-		entry->mode = one.mode;
-		entry->directory = S_ISDIR(one.mode) != 0;
-		entry->executable = (one.mode & S_IXUSR) != 0;
-		entry->symlink = S_ISLNK(one.mode) != 0;
-		entry->next = NULL;
-
-		*list_p = entry;
-		list_p = &entry->next;
-	}
-	return ret;
-}
-
-static int entcmp(const char *name1, int dir1, const char *name2, int dir2)
-{
-	int len1 = strlen(name1);
-	int len2 = strlen(name2);
-	int len = len1 < len2 ? len1 : len2;
-	int ret = memcmp(name1, name2, len);
-	unsigned char c1, c2;
-	if (ret)
-		return ret;
-	c1 = name1[len];
-	c2 = name2[len];
-	if (!c1 && dir1)
-		c1 = '/';
-	if (!c2 && dir2)
-		c2 = '/';
-	ret = (c1 < c2) ? -1 : (c1 > c2) ? 1 : 0;
-	if (c1 && c2 && !ret)
-		ret = len1 - len2;
-	return ret;
-}
-
-static int unpack_trees_rec(struct tree_entry_list **posns, int len,
-			    const char *base, merge_fn_t fn, int *indpos)
-{
-	int baselen = strlen(base);
-	int src_size = len + 1;
-	do {
-		int i;
-		const char *first;
-		int firstdir = 0;
-		int pathlen;
-		unsigned ce_size;
-		struct tree_entry_list **subposns;
-		struct cache_entry **src;
-		int any_files = 0;
-		int any_dirs = 0;
-		char *cache_name;
-		int ce_stage;
-
-		/* Find the first name in the input. */
-
-		first = NULL;
-		cache_name = NULL;
-
-		/* Check the cache */
-		if (merge && *indpos < active_nr) {
-			/* This is a bit tricky: */
-			/* If the index has a subdirectory (with
-			 * contents) as the first name, it'll get a
-			 * filename like "foo/bar". But that's after
-			 * "foo", so the entry in trees will get
-			 * handled first, at which point we'll go into
-			 * "foo", and deal with "bar" from the index,
-			 * because the base will be "foo/". The only
-			 * way we can actually have "foo/bar" first of
-			 * all the things is if the trees don't
-			 * contain "foo" at all, in which case we'll
-			 * handle "foo/bar" without going into the
-			 * directory, but that's fine (and will return
-			 * an error anyway, with the added unknown
-			 * file case.
-			 */
-
-			cache_name = active_cache[*indpos]->name;
-			if (strlen(cache_name) > baselen &&
-			    !memcmp(cache_name, base, baselen)) {
-				cache_name += baselen;
-				first = cache_name;
-			} else {
-				cache_name = NULL;
-			}
-		}
-
-#if DBRT_DEBUG > 1
-		if (first)
-			printf("index %s\n", first);
-#endif
-		for (i = 0; i < len; i++) {
-			if (!posns[i] || posns[i] == &df_conflict_list)
-				continue;
-#if DBRT_DEBUG > 1
-			printf("%d %s\n", i + 1, posns[i]->name);
-#endif
-			if (!first || entcmp(first, firstdir,
-					     posns[i]->name, 
-					     posns[i]->directory) > 0) {
-				first = posns[i]->name;
-				firstdir = posns[i]->directory;
-			}
-		}
-		/* No name means we're done */
-		if (!first)
-			return 0;
-
-		pathlen = strlen(first);
-		ce_size = cache_entry_size(baselen + pathlen);
-
-		src = xcalloc(src_size, sizeof(struct cache_entry *));
-
-		subposns = xcalloc(len, sizeof(struct tree_list_entry *));
-
-		if (cache_name && !strcmp(cache_name, first)) {
-			any_files = 1;
-			src[0] = active_cache[*indpos];
-			remove_cache_entry_at(*indpos);
-		}
-
-		for (i = 0; i < len; i++) {
-			struct cache_entry *ce;
-
-			if (!posns[i] ||
-			    (posns[i] != &df_conflict_list &&
-			     strcmp(first, posns[i]->name))) {
-				continue;
-			}
-
-			if (posns[i] == &df_conflict_list) {
-				src[i + merge] = &df_conflict_entry;
-				continue;
-			}
-
-			if (posns[i]->directory) {
-				struct tree *tree = lookup_tree(posns[i]->sha1);
-				any_dirs = 1;
-				parse_tree(tree);
-				subposns[i] = create_tree_entry_list(tree);
-				posns[i] = posns[i]->next;
-				src[i + merge] = &df_conflict_entry;
-				continue;
-			}
-
-			if (!merge)
-				ce_stage = 0;
-			else if (i + 1 < head_idx)
-				ce_stage = 1;
-			else if (i + 1 > head_idx)
-				ce_stage = 3;
-			else
-				ce_stage = 2;
-
-			ce = xcalloc(1, ce_size);
-			ce->ce_mode = create_ce_mode(posns[i]->mode);
-			ce->ce_flags = create_ce_flags(baselen + pathlen,
-						       ce_stage);
-			memcpy(ce->name, base, baselen);
-			memcpy(ce->name + baselen, first, pathlen + 1);
-
-			any_files = 1;
-
-			memcpy(ce->sha1, posns[i]->sha1, 20);
-			src[i + merge] = ce;
-			subposns[i] = &df_conflict_list;
-			posns[i] = posns[i]->next;
-		}
-		if (any_files) {
-			if (merge) {
-				int ret;
-
-#if DBRT_DEBUG > 1
-				printf("%s:\n", first);
-				for (i = 0; i < src_size; i++) {
-					printf(" %d ", i);
-					if (src[i])
-						printf("%s\n", sha1_to_hex(src[i]->sha1));
-					else
-						printf("\n");
-				}
-#endif
-				ret = fn(src);
-				
-#if DBRT_DEBUG > 1
-				printf("Added %d entries\n", ret);
-#endif
-				*indpos += ret;
-			} else {
-				for (i = 0; i < src_size; i++) {
-					if (src[i]) {
-						add_cache_entry(src[i], ADD_CACHE_OK_TO_ADD|ADD_CACHE_SKIP_DFCHECK);
-					}
-				}
-			}
-		}
-		if (any_dirs) {
-			char *newbase = xmalloc(baselen + 2 + pathlen);
-			memcpy(newbase, base, baselen);
-			memcpy(newbase + baselen, first, pathlen);
-			newbase[baselen + pathlen] = '/';
-			newbase[baselen + pathlen + 1] = '\0';
-			if (unpack_trees_rec(subposns, len, newbase, fn,
-					     indpos))
-				return -1;
-			free(newbase);
-		}
-		free(subposns);
-		free(src);
-	} while (1);
-}
-
-static void reject_merge(struct cache_entry *ce)
-{
-	die("Entry '%s' would be overwritten by merge. Cannot merge.", 
-	    ce->name);
-}
-
-/* Unlink the last component and attempt to remove leading
- * directories, in case this unlink is the removal of the
- * last entry in the directory -- empty directories are removed.
- */
-static void unlink_entry(char *name)
-{
-	char *cp, *prev;
-
-	if (unlink(name))
-		return;
-	prev = NULL;
-	while (1) {
-		int status;
-		cp = strrchr(name, '/');
-		if (prev)
-			*prev = '/';
-		if (!cp)
-			break;
-
-		*cp = 0;
-		status = rmdir(name);
-		if (status) {
-			*cp = '/';
-			break;
-		}
-		prev = cp;
-	}
-}
-
-static void progress_interval(int signum)
-{
-	progress_update = 1;
-}
-
-static void setup_progress_signal(void)
-{
-	struct sigaction sa;
-	struct itimerval v;
-
-	memset(&sa, 0, sizeof(sa));
-	sa.sa_handler = progress_interval;
-	sigemptyset(&sa.sa_mask);
-	sa.sa_flags = SA_RESTART;
-	sigaction(SIGALRM, &sa, NULL);
-
-	v.it_interval.tv_sec = 1;
-	v.it_interval.tv_usec = 0;
-	v.it_value = v.it_interval;
-	setitimer(ITIMER_REAL, &v, NULL);
-}
-
-static struct checkout state;
-static void check_updates(struct cache_entry **src, int nr)
-{
-	unsigned short mask = htons(CE_UPDATE);
-	unsigned last_percent = 200, cnt = 0, total = 0;
-
-	if (update && verbose_update) {
-		for (total = cnt = 0; cnt < nr; cnt++) {
-			struct cache_entry *ce = src[cnt];
-			if (!ce->ce_mode || ce->ce_flags & mask)
-				total++;
-		}
-
-		/* Don't bother doing this for very small updates */
-		if (total < 250)
-			total = 0;
-
-		if (total) {
-			fprintf(stderr, "Checking files out...\n");
-			setup_progress_signal();
-			progress_update = 1;
-		}
-		cnt = 0;
-	}
-
-	while (nr--) {
-		struct cache_entry *ce = *src++;
-
-		if (total) {
-			if (!ce->ce_mode || ce->ce_flags & mask) {
-				unsigned percent;
-				cnt++;
-				percent = (cnt * 100) / total;
-				if (percent != last_percent ||
-				    progress_update) {
-					fprintf(stderr, "%4u%% (%u/%u) done\r",
-						percent, cnt, total);
-					last_percent = percent;
-					progress_update = 0;
-				}
-			}
-		}
-		if (!ce->ce_mode) {
-			if (update)
-				unlink_entry(ce->name);
-			continue;
-		}
-		if (ce->ce_flags & mask) {
-			ce->ce_flags &= ~mask;
-			if (update)
-				checkout_entry(ce, &state, NULL);
-		}
-	}
-	if (total) {
-		signal(SIGALRM, SIG_IGN);
-		fputc('\n', stderr);
-	}
-}
-
-static int unpack_trees(merge_fn_t fn)
-{
-	int indpos = 0;
-	unsigned len = object_list_length(trees);
-	struct tree_entry_list **posns;
-	int i;
-	struct object_list *posn = trees;
-	merge_size = len;
-
-	if (len) {
-		posns = xmalloc(len * sizeof(struct tree_entry_list *));
-		for (i = 0; i < len; i++) {
-			posns[i] = create_tree_entry_list((struct tree *) posn->item);
-			posn = posn->next;
-		}
-		if (unpack_trees_rec(posns, len, prefix ? prefix : "",
-				     fn, &indpos))
-			return -1;
-	}
-
-	if (trivial_merges_only && nontrivial_merge)
-		die("Merge requires file-level merging");
-
-	check_updates(active_cache, active_nr);
-	return 0;
-}
-
 static int list_tree(unsigned char *sha1)
 {
 	struct tree *tree = parse_tree_indirect(sha1);
@@ -425,386 +23,6 @@ static int list_tree(unsigned char *sha1)
 	return 0;
 }
 
-static int same(struct cache_entry *a, struct cache_entry *b)
-{
-	if (!!a != !!b)
-		return 0;
-	if (!a && !b)
-		return 1;
-	return a->ce_mode == b->ce_mode && 
-		!memcmp(a->sha1, b->sha1, 20);
-}
-
-
-/*
- * When a CE gets turned into an unmerged entry, we
- * want it to be up-to-date
- */
-static void verify_uptodate(struct cache_entry *ce)
-{
-	struct stat st;
-
-	if (index_only || reset)
-		return;
-
-	if (!lstat(ce->name, &st)) {
-		unsigned changed = ce_match_stat(ce, &st, 1);
-		if (!changed)
-			return;
-		errno = 0;
-	}
-	if (reset) {
-		ce->ce_flags |= htons(CE_UPDATE);
-		return;
-	}
-	if (errno == ENOENT)
-		return;
-	die("Entry '%s' not uptodate. Cannot merge.", ce->name);
-}
-
-static void invalidate_ce_path(struct cache_entry *ce)
-{
-	if (ce)
-		cache_tree_invalidate_path(active_cache_tree, ce->name);
-}
-
-/*
- * We do not want to remove or overwrite a working tree file that
- * is not tracked.
- */
-static void verify_absent(const char *path, const char *action)
-{
-	struct stat st;
-
-	if (index_only || reset || !update)
-		return;
-	if (!lstat(path, &st))
-		die("Untracked working tree file '%s' "
-		    "would be %s by merge.", path, action);
-}
-
-static int merged_entry(struct cache_entry *merge, struct cache_entry *old)
-{
-	merge->ce_flags |= htons(CE_UPDATE);
-	if (old) {
-		/*
-		 * See if we can re-use the old CE directly?
-		 * That way we get the uptodate stat info.
-		 *
-		 * This also removes the UPDATE flag on
-		 * a match.
-		 */
-		if (same(old, merge)) {
-			*merge = *old;
-		} else {
-			verify_uptodate(old);
-			invalidate_ce_path(old);
-		}
-	}
-	else {
-		verify_absent(merge->name, "overwritten");
-		invalidate_ce_path(merge);
-	}
-
-	merge->ce_flags &= ~htons(CE_STAGEMASK);
-	add_cache_entry(merge, ADD_CACHE_OK_TO_ADD);
-	return 1;
-}
-
-static int deleted_entry(struct cache_entry *ce, struct cache_entry *old)
-{
-	if (old)
-		verify_uptodate(old);
-	else
-		verify_absent(ce->name, "removed");
-	ce->ce_mode = 0;
-	add_cache_entry(ce, ADD_CACHE_OK_TO_ADD);
-	invalidate_ce_path(ce);
-	return 1;
-}
-
-static int keep_entry(struct cache_entry *ce)
-{
-	add_cache_entry(ce, ADD_CACHE_OK_TO_ADD);
-	return 1;
-}
-
-#if DBRT_DEBUG
-static void show_stage_entry(FILE *o,
-			     const char *label, const struct cache_entry *ce)
-{
-	if (!ce)
-		fprintf(o, "%s (missing)\n", label);
-	else
-		fprintf(o, "%s%06o %s %d\t%s\n",
-			label,
-			ntohl(ce->ce_mode),
-			sha1_to_hex(ce->sha1),
-			ce_stage(ce),
-			ce->name);
-}
-#endif
-
-static int threeway_merge(struct cache_entry **stages)
-{
-	struct cache_entry *index;
-	struct cache_entry *head; 
-	struct cache_entry *remote = stages[head_idx + 1];
-	int count;
-	int head_match = 0;
-	int remote_match = 0;
-	const char *path = NULL;
-
-	int df_conflict_head = 0;
-	int df_conflict_remote = 0;
-
-	int any_anc_missing = 0;
-	int no_anc_exists = 1;
-	int i;
-
-	for (i = 1; i < head_idx; i++) {
-		if (!stages[i])
-			any_anc_missing = 1;
-		else {
-			if (!path)
-				path = stages[i]->name;
-			no_anc_exists = 0;
-		}
-	}
-
-	index = stages[0];
-	head = stages[head_idx];
-
-	if (head == &df_conflict_entry) {
-		df_conflict_head = 1;
-		head = NULL;
-	}
-
-	if (remote == &df_conflict_entry) {
-		df_conflict_remote = 1;
-		remote = NULL;
-	}
-
-	if (!path && index)
-		path = index->name;
-	if (!path && head)
-		path = head->name;
-	if (!path && remote)
-		path = remote->name;
-
-	/* First, if there's a #16 situation, note that to prevent #13
-	 * and #14.
-	 */
-	if (!same(remote, head)) {
-		for (i = 1; i < head_idx; i++) {
-			if (same(stages[i], head)) {
-				head_match = i;
-			}
-			if (same(stages[i], remote)) {
-				remote_match = i;
-			}
-		}
-	}
-
-	/* We start with cases where the index is allowed to match
-	 * something other than the head: #14(ALT) and #2ALT, where it
-	 * is permitted to match the result instead.
-	 */
-	/* #14, #14ALT, #2ALT */
-	if (remote && !df_conflict_head && head_match && !remote_match) {
-		if (index && !same(index, remote) && !same(index, head))
-			reject_merge(index);
-		return merged_entry(remote, index);
-	}
-	/*
-	 * If we have an entry in the index cache, then we want to
-	 * make sure that it matches head.
-	 */
-	if (index && !same(index, head)) {
-		reject_merge(index);
-	}
-
-	if (head) {
-		/* #5ALT, #15 */
-		if (same(head, remote))
-			return merged_entry(head, index);
-		/* #13, #3ALT */
-		if (!df_conflict_remote && remote_match && !head_match)
-			return merged_entry(head, index);
-	}
-
-	/* #1 */
-	if (!head && !remote && any_anc_missing)
-		return 0;
-
-	/* Under the new "aggressive" rule, we resolve mostly trivial
-	 * cases that we historically had git-merge-one-file resolve.
-	 */
-	if (aggressive) {
-		int head_deleted = !head && !df_conflict_head;
-		int remote_deleted = !remote && !df_conflict_remote;
-		/*
-		 * Deleted in both.
-		 * Deleted in one and unchanged in the other.
-		 */
-		if ((head_deleted && remote_deleted) ||
-		    (head_deleted && remote && remote_match) ||
-		    (remote_deleted && head && head_match)) {
-			if (index)
-				return deleted_entry(index, index);
-			else if (path)
-				verify_absent(path, "removed");
-			return 0;
-		}
-		/*
-		 * Added in both, identically.
-		 */
-		if (no_anc_exists && head && remote && same(head, remote))
-			return merged_entry(head, index);
-
-	}
-
-	/* Below are "no merge" cases, which require that the index be
-	 * up-to-date to avoid the files getting overwritten with
-	 * conflict resolution files. 
-	 */
-	if (index) {
-		verify_uptodate(index);
-	}
-	else if (path)
-		verify_absent(path, "overwritten");
-
-	nontrivial_merge = 1;
-
-	/* #2, #3, #4, #6, #7, #9, #11. */
-	count = 0;
-	if (!head_match || !remote_match) {
-		for (i = 1; i < head_idx; i++) {
-			if (stages[i]) {
-				keep_entry(stages[i]);
-				count++;
-				break;
-			}
-		}
-	}
-#if DBRT_DEBUG
-	else {
-		fprintf(stderr, "read-tree: warning #16 detected\n");
-		show_stage_entry(stderr, "head   ", stages[head_match]);
-		show_stage_entry(stderr, "remote ", stages[remote_match]);
-	}
-#endif
-	if (head) { count += keep_entry(head); }
-	if (remote) { count += keep_entry(remote); }
-	return count;
-}
-
-/*
- * Two-way merge.
- *
- * The rule is to "carry forward" what is in the index without losing
- * information across a "fast forward", favoring a successful merge
- * over a merge failure when it makes sense.  For details of the
- * "carry forward" rule, please see <Documentation/git-read-tree.txt>.
- *
- */
-static int twoway_merge(struct cache_entry **src)
-{
-	struct cache_entry *current = src[0];
-	struct cache_entry *oldtree = src[1], *newtree = src[2];
-
-	if (merge_size != 2)
-		return error("Cannot do a twoway merge of %d trees",
-			     merge_size);
-
-	if (current) {
-		if ((!oldtree && !newtree) || /* 4 and 5 */
-		    (!oldtree && newtree &&
-		     same(current, newtree)) || /* 6 and 7 */
-		    (oldtree && newtree &&
-		     same(oldtree, newtree)) || /* 14 and 15 */
-		    (oldtree && newtree &&
-		     !same(oldtree, newtree) && /* 18 and 19*/
-		     same(current, newtree))) {
-			return keep_entry(current);
-		}
-		else if (oldtree && !newtree && same(current, oldtree)) {
-			/* 10 or 11 */
-			return deleted_entry(oldtree, current);
-		}
-		else if (oldtree && newtree &&
-			 same(current, oldtree) && !same(current, newtree)) {
-			/* 20 or 21 */
-			return merged_entry(newtree, current);
-		}
-		else {
-			/* all other failures */
-			if (oldtree)
-				reject_merge(oldtree);
-			if (current)
-				reject_merge(current);
-			if (newtree)
-				reject_merge(newtree);
-			return -1;
-		}
-	}
-	else if (newtree)
-		return merged_entry(newtree, current);
-	else
-		return deleted_entry(oldtree, current);
-}
-
-/*
- * Bind merge.
- *
- * Keep the index entries at stage0, collapse stage1 but make sure
- * stage0 does not have anything there.
- */
-static int bind_merge(struct cache_entry **src)
-{
-	struct cache_entry *old = src[0];
-	struct cache_entry *a = src[1];
-
-	if (merge_size != 1)
-		return error("Cannot do a bind merge of %d trees\n",
-			     merge_size);
-	if (a && old)
-		die("Entry '%s' overlaps.  Cannot bind.", a->name);
-	if (!a)
-		return keep_entry(old);
-	else
-		return merged_entry(a, NULL);
-}
-
-/*
- * One-way merge.
- *
- * The rule is:
- * - take the stat information from stage0, take the data from stage1
- */
-static int oneway_merge(struct cache_entry **src)
-{
-	struct cache_entry *old = src[0];
-	struct cache_entry *a = src[1];
-
-	if (merge_size != 1)
-		return error("Cannot do a oneway merge of %d trees",
-			     merge_size);
-
-	if (!a)
-		return deleted_entry(old, old);
-	if (old && same(old, a)) {
-		if (reset) {
-			struct stat st;
-			if (lstat(old->name, &st) ||
-			    ce_match_stat(old, &st, 1))
-				old->ce_flags |= htons(CE_UPDATE);
-		}
-		return keep_entry(old);
-	}
-	return merged_entry(a, old);
-}
-
 static int read_cache_unmerged(void)
 {
 	int i;
@@ -818,7 +36,7 @@ static int read_cache_unmerged(void)
 		if (ce_stage(ce)) {
 			if (last && !strcmp(ce->name, last->name))
 				continue;
-			invalidate_ce_path(ce);
+			cache_tree_invalidate_path(active_cache_tree, ce->name);
 			last = ce;
 			ce->ce_mode = 0;
 			ce->ce_flags &= ~htons(CE_STAGEMASK);
@@ -870,17 +88,14 @@ static const char read_tree_usage[] = "git-read-tree (<sha> | [[-m [--aggressive
 
 static struct lock_file lock_file;
 
-int cmd_read_tree(int argc, const char **argv, char **envp)
+int cmd_read_tree(int argc, const char **argv, const char *prefix)
 {
 	int i, newfd, stage = 0;
 	unsigned char sha1[20];
-	merge_fn_t fn = NULL;
+	struct unpack_trees_options opts;
 
-	df_conflict_list.next = &df_conflict_list;
-	state.base_dir = "";
-	state.force = 1;
-	state.quiet = 1;
-	state.refresh_cache = 1;
+	memset(&opts, 0, sizeof(opts));
+	opts.head_idx = -1;
 
 	setup_git_directory();
 	git_config(git_default_config);
@@ -891,8 +106,6 @@ int cmd_read_tree(int argc, const char **argv, char **envp)
 
 	git_config(git_default_config);
 
-	merge = 0;
-	reset = 0;
 	for (i = 1; i < argc; i++) {
 		const char *arg = argv[i];
 
@@ -900,12 +113,12 @@ int cmd_read_tree(int argc, const char **argv, char **envp)
 		 * the working tree.
 		 */
 		if (!strcmp(arg, "-u")) {
-			update = 1;
+			opts.update = 1;
 			continue;
 		}
 
 		if (!strcmp(arg, "-v")) {
-			verbose_update = 1;
+			opts.verbose_update = 1;
 			continue;
 		}
 
@@ -913,7 +126,7 @@ int cmd_read_tree(int argc, const char **argv, char **envp)
 		 * not even look at the working tree.
 		 */
 		if (!strcmp(arg, "-i")) {
-			index_only = 1;
+			opts.index_only = 1;
 			continue;
 		}
 
@@ -922,10 +135,10 @@ int cmd_read_tree(int argc, const char **argv, char **envp)
 		 * given subdirectory.
 		 */
 		if (!strncmp(arg, "--prefix=", 9)) {
-			if (stage || merge || prefix)
+			if (stage || opts.merge || opts.prefix)
 				usage(read_tree_usage);
-			prefix = arg + 9;
-			merge = 1;
+			opts.prefix = arg + 9;
+			opts.merge = 1;
 			stage = 1;
 			if (read_cache_unmerged())
 				die("you need to resolve your current index first");
@@ -937,38 +150,38 @@ int cmd_read_tree(int argc, const char **argv, char **envp)
 		 * correspond to them.
 		 */
 		if (!strcmp(arg, "--reset")) {
-			if (stage || merge || prefix)
+			if (stage || opts.merge || opts.prefix)
 				usage(read_tree_usage);
-			reset = 1;
-			merge = 1;
+			opts.reset = 1;
+			opts.merge = 1;
 			stage = 1;
 			read_cache_unmerged();
 			continue;
 		}
 
 		if (!strcmp(arg, "--trivial")) {
-			trivial_merges_only = 1;
+			opts.trivial_merges_only = 1;
 			continue;
 		}
 
 		if (!strcmp(arg, "--aggressive")) {
-			aggressive = 1;
+			opts.aggressive = 1;
 			continue;
 		}
 
 		/* "-m" stands for "merge", meaning we start in stage 1 */
 		if (!strcmp(arg, "-m")) {
-			if (stage || merge || prefix)
+			if (stage || opts.merge || opts.prefix)
 				usage(read_tree_usage);
 			if (read_cache_unmerged())
 				die("you need to resolve your current index first");
 			stage = 1;
-			merge = 1;
+			opts.merge = 1;
 			continue;
 		}
 
 		/* using -u and -i at the same time makes no sense */
-		if (1 < index_only + update)
+		if (1 < opts.index_only + opts.update)
 			usage(read_tree_usage);
 
 		if (get_sha1(arg, sha1))
@@ -977,52 +190,53 @@ int cmd_read_tree(int argc, const char **argv, char **envp)
 			die("failed to unpack tree object %s", arg);
 		stage++;
 	}
-	if ((update||index_only) && !merge)
+	if ((opts.update||opts.index_only) && !opts.merge)
 		usage(read_tree_usage);
 
-	if (prefix) {
-		int pfxlen = strlen(prefix);
+	if (opts.prefix) {
+		int pfxlen = strlen(opts.prefix);
 		int pos;
-		if (prefix[pfxlen-1] != '/')
+		if (opts.prefix[pfxlen-1] != '/')
 			die("prefix must end with /");
 		if (stage != 2)
 			die("binding merge takes only one tree");
-		pos = cache_name_pos(prefix, pfxlen);
+		pos = cache_name_pos(opts.prefix, pfxlen);
 		if (0 <= pos)
 			die("corrupt index file");
 		pos = -pos-1;
 		if (pos < active_nr &&
-		    !strncmp(active_cache[pos]->name, prefix, pfxlen))
-			die("subdirectory '%s' already exists.", prefix);
-		pos = cache_name_pos(prefix, pfxlen-1);
+		    !strncmp(active_cache[pos]->name, opts.prefix, pfxlen))
+			die("subdirectory '%s' already exists.", opts.prefix);
+		pos = cache_name_pos(opts.prefix, pfxlen-1);
 		if (0 <= pos)
-			die("file '%.*s' already exists.", pfxlen-1, prefix);
+			die("file '%.*s' already exists.",
+					pfxlen-1, opts.prefix);
 	}
 
-	if (merge) {
+	if (opts.merge) {
 		if (stage < 2)
 			die("just how do you expect me to merge %d trees?", stage-1);
 		switch (stage - 1) {
 		case 1:
-			fn = prefix ? bind_merge : oneway_merge;
+			opts.fn = opts.prefix ? bind_merge : oneway_merge;
 			break;
 		case 2:
-			fn = twoway_merge;
+			opts.fn = twoway_merge;
 			break;
 		case 3:
 		default:
-			fn = threeway_merge;
+			opts.fn = threeway_merge;
 			cache_tree_free(&active_cache_tree);
 			break;
 		}
 
 		if (stage - 1 >= 3)
-			head_idx = stage - 2;
+			opts.head_idx = stage - 2;
 		else
-			head_idx = 1;
+			opts.head_idx = 1;
 	}
 
-	unpack_trees(fn);
+	unpack_trees(trees, &opts);
 
 	/*
 	 * When reading only one tree (either the most basic form,
@@ -1030,7 +244,7 @@ int cmd_read_tree(int argc, const char **argv, char **envp)
 	 * valid cache-tree because the index must match exactly
 	 * what came from the tree.
 	 */
-	if (trees && trees->item && !prefix && (!merge || (stage == 2))) {
+	if (trees && trees->item && !opts.prefix && (!opts.merge || (stage == 2))) {
 		cache_tree_free(&active_cache_tree);
 		prime_cache_tree();
 	}
diff --git a/builtin-rev-list.c b/builtin-rev-list.c
index 8f32871337..0dee1734a3 100644
--- a/builtin-rev-list.c
+++ b/builtin-rev-list.c
@@ -306,12 +306,12 @@ static void mark_edges_uninteresting(struct commit_list *list)
 	}
 }
 
-int cmd_rev_list(int argc, const char **argv, char **envp)
+int cmd_rev_list(int argc, const char **argv, const char *prefix)
 {
 	struct commit_list *list;
 	int i;
 
-	init_revisions(&revs);
+	init_revisions(&revs, prefix);
 	revs.abbrev = 0;
 	revs.commit_format = CMIT_FMT_UNSPECIFIED;
 	argc = setup_revisions(argc, argv, &revs, NULL);
diff --git a/builtin-rev-parse.c b/builtin-rev-parse.c
index b3e4386c1b..aca4a36032 100644
--- a/builtin-rev-parse.c
+++ b/builtin-rev-parse.c
@@ -209,11 +209,10 @@ static int try_difference(const char *arg)
 	return 0;
 }
 
-int cmd_rev_parse(int argc, const char **argv, char **envp)
+int cmd_rev_parse(int argc, const char **argv, const char *prefix)
 {
 	int i, as_is = 0, verify = 0;
 	unsigned char sha1[20];
-	const char *prefix = setup_git_directory();
 
 	git_config(git_default_config);
 
diff --git a/builtin-rm.c b/builtin-rm.c
index 5deb811719..92d205a715 100644
--- a/builtin-rm.c
+++ b/builtin-rm.c
@@ -43,11 +43,10 @@ static int remove_file(const char *name)
 
 static struct lock_file lock_file;
 
-int cmd_rm(int argc, const char **argv, char **envp)
+int cmd_rm(int argc, const char **argv, const char *prefix)
 {
 	int i, newfd;
 	int verbose = 0, show_only = 0, force = 0;
-	const char *prefix = setup_git_directory();
 	const char **pathspec;
 	char *seen;
 
@@ -90,8 +89,7 @@ int cmd_rm(int argc, const char **argv, char **envp)
 	seen = NULL;
 	for (i = 0; pathspec[i] ; i++)
 		/* nothing */;
-	seen = xmalloc(i);
-	memset(seen, 0, i);
+	seen = xcalloc(i, 1);
 
 	for (i = 0; i < active_nr; i++) {
 		struct cache_entry *ce = active_cache[i];
diff --git a/builtin-show-branch.c b/builtin-show-branch.c
index 260cb221b9..2a1b848f6c 100644
--- a/builtin-show-branch.c
+++ b/builtin-show-branch.c
@@ -89,6 +89,8 @@ static int name_first_parent_chain(struct commit *c)
 			name_parent(c, p);
 			i++;
 		}
+		else
+			break;
 		c = p;
 	}
 	return i;
@@ -172,7 +174,7 @@ static void name_commits(struct commit_list *list,
 static int mark_seen(struct commit *commit, struct commit_list **seen_p)
 {
 	if (!commit->object.flags) {
-		insert_by_date(commit, seen_p);
+		commit_list_insert(commit, seen_p);
 		return 1;
 	}
 	return 0;
@@ -218,9 +220,8 @@ static void join_revs(struct commit_list **list_p,
 	 * Postprocess to complete well-poisoning.
 	 *
 	 * At this point we have all the commits we have seen in
-	 * seen_p list (which happens to be sorted chronologically but
-	 * it does not really matter).  Mark anything that can be
-	 * reached from uninteresting commits not interesting.
+	 * seen_p list.  Mark anything that can be reached from
+	 * uninteresting commits not interesting.
 	 */
 	for (;;) {
 		int changed = 0;
@@ -549,7 +550,7 @@ static int omit_in_dense(struct commit *commit, struct commit **rev, int n)
 	return 0;
 }
 
-int cmd_show_branch(int ac, const char **av, char **envp)
+int cmd_show_branch(int ac, const char **av, const char *prefix)
 {
 	struct commit *rev[MAX_REVS], *commit;
 	struct commit_list *list = NULL, *seen = NULL;
@@ -572,7 +573,6 @@ int cmd_show_branch(int ac, const char **av, char **envp)
 	int topics = 0;
 	int dense = 1;
 
-	setup_git_directory();
 	git_config(git_show_branch_config);
 
 	/* If nothing is specified, try the default first */
@@ -701,6 +701,8 @@ int cmd_show_branch(int ac, const char **av, char **envp)
 	if (0 <= extra)
 		join_revs(&list, &seen, num_rev, extra);
 
+	sort_by_date(&seen);
+
 	if (merge_base)
 		return show_merge_base(seen, num_rev);
 
diff --git a/builtin-stripspace.c b/builtin-stripspace.c
index 2ce1264f7b..09cc9108cd 100644
--- a/builtin-stripspace.c
+++ b/builtin-stripspace.c
@@ -54,7 +54,7 @@ void stripspace(FILE *in, FILE *out)
 		fputc('\n', out);
 }
 
-int cmd_stripspace(int argc, const char **argv, char **envp)
+int cmd_stripspace(int argc, const char **argv, const char *prefix)
 {
 	stripspace(stdin, stdout);
 	return 0;
diff --git a/builtin-tar-tree.c b/builtin-tar-tree.c
index f2e48aae2a..7c48db9ec8 100644
--- a/builtin-tar-tree.c
+++ b/builtin-tar-tree.c
@@ -20,6 +20,7 @@ static char block[BLOCKSIZE];
 static unsigned long offset;
 
 static time_t archive_time;
+static int tar_umask;
 
 /* tries hard to write, either succeeds or dies in the attempt */
 static void reliable_write(const void *data, unsigned long size)
@@ -188,13 +189,13 @@ static void write_entry(const unsigned char *sha1, struct strbuf *path,
 	} else {
 		if (S_ISDIR(mode)) {
 			*header.typeflag = TYPEFLAG_DIR;
-			mode |= 0777;
+			mode = (mode | 0777) & ~tar_umask;
 		} else if (S_ISLNK(mode)) {
 			*header.typeflag = TYPEFLAG_LNK;
 			mode |= 0777;
 		} else if (S_ISREG(mode)) {
 			*header.typeflag = TYPEFLAG_REG;
-			mode |= (mode & 0100) ? 0777 : 0666;
+			mode = (mode | ((mode & 0100) ? 0777 : 0666)) & ~tar_umask;
 		} else {
 			error("unsupported file mode: 0%o (SHA1: %s)",
 			      mode, sha1_to_hex(sha1));
@@ -293,7 +294,21 @@ static void traverse_tree(struct tree_desc *tree, struct strbuf *path)
 	}
 }
 
-static int generate_tar(int argc, const char **argv, char** envp)
+int git_tar_config(const char *var, const char *value)
+{
+	if (!strcmp(var, "tar.umask")) {
+		if (!strcmp(value, "user")) {
+			tar_umask = umask(0);
+			umask(tar_umask);
+		} else {
+			tar_umask = git_config_int(var, value);
+		}
+		return 0;
+	}
+	return git_default_config(var, value);
+}
+
+static int generate_tar(int argc, const char **argv, const char *prefix)
 {
 	unsigned char sha1[20], tree_sha1[20];
 	struct commit *commit;
@@ -304,8 +319,7 @@ static int generate_tar(int argc, const char **argv, char** envp)
 	current_path.alloc = PATH_MAX;
 	current_path.len = current_path.eof = 0;
 
-	setup_git_directory();
-	git_config(git_default_config);
+	git_config(git_tar_config);
 
 	switch (argc) {
 	case 3:
@@ -387,19 +401,19 @@ static int remote_tar(int argc, const char **argv)
 	return !!ret;
 }
 
-int cmd_tar_tree(int argc, const char **argv, char **envp)
+int cmd_tar_tree(int argc, const char **argv, const char *prefix)
 {
 	if (argc < 2)
 		usage(tar_tree_usage);
 	if (!strncmp("--remote=", argv[1], 9))
 		return remote_tar(argc, argv);
-	return generate_tar(argc, argv, envp);
+	return generate_tar(argc, argv, prefix);
 }
 
 /* ustar header + extended global header content */
 #define HEADERSIZE (2 * RECORDSIZE)
 
-int cmd_get_tar_commit_id(int argc, const char **argv, char **envp)
+int cmd_get_tar_commit_id(int argc, const char **argv, const char *prefix)
 {
 	char buffer[HEADERSIZE];
 	struct ustar_header *header = (struct ustar_header *)buffer;
diff --git a/builtin-update-index.c b/builtin-update-index.c
index 1a4200d151..24dca47d8d 100644
--- a/builtin-update-index.c
+++ b/builtin-update-index.c
@@ -476,12 +476,11 @@ static int do_reupdate(int ac, const char **av,
 	return 0;
 }
 
-int cmd_update_index(int argc, const char **argv, char **envp)
+int cmd_update_index(int argc, const char **argv, const char *prefix)
 {
 	int i, newfd, entries, has_errors = 0, line_termination = '\n';
 	int allow_options = 1;
 	int read_from_stdin = 0;
-	const char *prefix = setup_git_directory();
 	int prefix_length = prefix ? strlen(prefix) : 0;
 	char set_executable_bit = 0;
 	unsigned int refresh_flags = 0;
diff --git a/builtin-update-ref.c b/builtin-update-ref.c
index 83094abe0f..5bd71825fd 100644
--- a/builtin-update-ref.c
+++ b/builtin-update-ref.c
@@ -5,7 +5,7 @@
 static const char git_update_ref_usage[] =
 "git-update-ref <refname> <value> [<oldval>] [-m <reason>]";
 
-int cmd_update_ref(int argc, const char **argv, char **envp)
+int cmd_update_ref(int argc, const char **argv, const char *prefix)
 {
 	const char *refname=NULL, *value=NULL, *oldval=NULL, *msg=NULL;
 	struct ref_lock *lock;
@@ -13,7 +13,6 @@ int cmd_update_ref(int argc, const char **argv, char **envp)
 	int i;
 
 	setup_ident();
-	setup_git_directory();
 	git_config(git_default_config);
 
 	for (i = 1; i < argc; i++) {
diff --git a/builtin-upload-tar.c b/builtin-upload-tar.c
index d4fa7b56c3..7b401bbb77 100644
--- a/builtin-upload-tar.c
+++ b/builtin-upload-tar.c
@@ -15,7 +15,7 @@ static int nak(const char *reason)
 	return 1;
 }
 
-int cmd_upload_tar(int argc, const char **argv, char **envp)
+int cmd_upload_tar(int argc, const char **argv, const char *prefix)
 {
 	int len;
 	const char *dir = argv[1];
diff --git a/builtin-write-tree.c b/builtin-write-tree.c
index 449a4d1b57..0289f59936 100644
--- a/builtin-write-tree.c
+++ b/builtin-write-tree.c
@@ -60,14 +60,12 @@ int write_tree(unsigned char *sha1, int missing_ok, const char *prefix)
 	return 0;
 }
 
-int cmd_write_tree(int argc, const char **argv, char **envp)
+int cmd_write_tree(int argc, const char **argv, const char *unused_prefix)
 {
 	int missing_ok = 0, ret;
 	const char *prefix = NULL;
 	unsigned char sha1[20];
 
-	setup_git_directory();
-
 	while (1 < argc) {
 		const char *arg = argv[1];
 		if (!strcmp(arg, "--missing-ok"))
diff --git a/builtin.h b/builtin.h
index 5339d8627f..1c8637ae22 100644
--- a/builtin.h
+++ b/builtin.h
@@ -15,53 +15,54 @@ void cmd_usage(int show_all, const char *exec_path, const char *fmt, ...)
 #endif
 	;
 
-extern int cmd_help(int argc, const char **argv, char **envp);
-extern int cmd_version(int argc, const char **argv, char **envp);
+extern int cmd_help(int argc, const char **argv, const char *prefix);
+extern int cmd_version(int argc, const char **argv, const char *prefix);
 
-extern int cmd_whatchanged(int argc, const char **argv, char **envp);
-extern int cmd_show(int argc, const char **argv, char **envp);
-extern int cmd_log(int argc, const char **argv, char **envp);
-extern int cmd_diff(int argc, const char **argv, char **envp);
-extern int cmd_format_patch(int argc, const char **argv, char **envp);
-extern int cmd_count_objects(int argc, const char **argv, char **envp);
+extern int cmd_whatchanged(int argc, const char **argv, const char *prefix);
+extern int cmd_show(int argc, const char **argv, const char *prefix);
+extern int cmd_log(int argc, const char **argv, const char *prefix);
+extern int cmd_diff(int argc, const char **argv, const char *prefix);
+extern int cmd_format_patch(int argc, const char **argv, const char *prefix);
+extern int cmd_count_objects(int argc, const char **argv, const char *prefix);
 
-extern int cmd_prune(int argc, const char **argv, char **envp);
+extern int cmd_prune(int argc, const char **argv, const char *prefix);
 
-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_rm(int argc, const char **argv, char **envp);
-extern int cmd_add(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);
-extern int cmd_tar_tree(int argc, const char **argv, char **envp);
-extern int cmd_upload_tar(int argc, const char **argv, char **envp);
-extern int cmd_get_tar_commit_id(int argc, const char **argv, char **envp);
-extern int cmd_ls_files(int argc, const char **argv, char **envp);
-extern int cmd_ls_tree(int argc, const char **argv, char **envp);
-extern int cmd_read_tree(int argc, const char **argv, char **envp);
-extern int cmd_commit_tree(int argc, const char **argv, char **envp);
-extern int cmd_apply(int argc, const char **argv, char **envp);
-extern int cmd_show_branch(int argc, const char **argv, char **envp);
-extern int cmd_diff_files(int argc, const char **argv, char **envp);
-extern int cmd_diff_index(int argc, const char **argv, char **envp);
-extern int cmd_diff_stages(int argc, const char **argv, char **envp);
-extern int cmd_diff_tree(int argc, const char **argv, char **envp);
-extern int cmd_cat_file(int argc, const char **argv, char **envp);
-extern int cmd_rev_parse(int argc, const char **argv, char **envp);
-extern int cmd_update_index(int argc, const char **argv, char **envp);
-extern int cmd_update_ref(int argc, const char **argv, char **envp);
-extern int cmd_fmt_merge_msg(int argc, const char **argv, char **envp);
+extern int cmd_push(int argc, const char **argv, const char *prefix);
+extern int cmd_grep(int argc, const char **argv, const char *prefix);
+extern int cmd_rm(int argc, const char **argv, const char *prefix);
+extern int cmd_add(int argc, const char **argv, const char *prefix);
+extern int cmd_rev_list(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_init_db(int argc, const char **argv, const char *prefix);
+extern int cmd_tar_tree(int argc, const char **argv, const char *prefix);
+extern int cmd_upload_tar(int argc, const char **argv, const char *prefix);
+extern int cmd_get_tar_commit_id(int argc, const char **argv, const char *prefix);
+extern int cmd_ls_files(int argc, const char **argv, const char *prefix);
+extern int cmd_ls_tree(int argc, const char **argv, const char *prefix);
+extern int cmd_read_tree(int argc, const char **argv, const char *prefix);
+extern int cmd_commit_tree(int argc, const char **argv, const char *prefix);
+extern int cmd_apply(int argc, const char **argv, const char *prefix);
+extern int cmd_show_branch(int argc, const char **argv, const char *prefix);
+extern int cmd_diff_files(int argc, const char **argv, const char *prefix);
+extern int cmd_diff_index(int argc, const char **argv, const char *prefix);
+extern int cmd_diff_stages(int argc, const char **argv, const char *prefix);
+extern int cmd_diff_tree(int argc, const char **argv, const char *prefix);
+extern int cmd_cat_file(int argc, const char **argv, const char *prefix);
+extern int cmd_rev_parse(int argc, const char **argv, const char *prefix);
+extern int cmd_update_index(int argc, const char **argv, const char *prefix);
+extern int cmd_update_ref(int argc, const char **argv, const char *prefix);
+extern int cmd_fmt_merge_msg(int argc, const char **argv, const char *prefix);
+extern int cmd_mv(int argc, const char **argv, const char *prefix);
 
-extern int cmd_write_tree(int argc, const char **argv, char **envp);
+extern int cmd_write_tree(int argc, const char **argv, const char *prefix);
 extern int write_tree(unsigned char *sha1, int missing_ok, const char *prefix);
 
-extern int cmd_mailsplit(int argc, const char **argv, char **envp);
+extern int cmd_mailsplit(int argc, const char **argv, const char *prefix);
 extern int split_mbox(const char **mbox, const char *dir, int allow_bare, int nr_prec, int skip);
 
-extern int cmd_mailinfo(int argc, const char **argv, char **envp);
+extern int cmd_mailinfo(int argc, const char **argv, const char *prefix);
 extern int mailinfo(FILE *in, FILE *out, int ks, const char *encoding, const char *msg, const char *patch);
 
-extern int cmd_stripspace(int argc, const char **argv, char **envp);
+extern int cmd_stripspace(int argc, const char **argv, const char *prefix);
 extern void stripspace(FILE *in, FILE *out);
 #endif
diff --git a/cache.h b/cache.h
index 8cc0ccbd0f..7c69b30637 100644
--- a/cache.h
+++ b/cache.h
@@ -155,6 +155,7 @@ extern int add_cache_entry(struct cache_entry *ce, int option);
 extern struct cache_entry *refresh_cache_entry(struct cache_entry *ce, int really);
 extern int remove_cache_entry_at(int pos);
 extern int remove_file_from_cache(const char *path);
+extern int add_file_to_index(const char *path, int verbose);
 extern int ce_same_name(struct cache_entry *a, struct cache_entry *b);
 extern int ce_match_stat(struct cache_entry *ce, struct stat *st, int);
 extern int ce_modified(struct cache_entry *ce, struct stat *st, int);
@@ -180,6 +181,7 @@ extern int commit_lock_file(struct lock_file *);
 extern void rollback_lock_file(struct lock_file *);
 
 /* Environment bits from configuration mechanism */
+extern int use_legacy_headers;
 extern int trust_executable_bit;
 extern int assume_unchanged;
 extern int prefer_symlink_refs;
diff --git a/combine-diff.c b/combine-diff.c
index 1bc1484645..919112bba9 100644
--- a/combine-diff.c
+++ b/combine-diff.c
@@ -639,8 +639,7 @@ static int show_patch_diff(struct combine_diff_path *elem, int num_parent,
 			/* deleted file */
 			result_size = 0;
 			elem->mode = 0;
-			result = xmalloc(1);
-			result[0] = 0;
+			result = xcalloc(1, 1);
 		}
 		if (0 <= fd)
 			close(fd);
diff --git a/config.c b/config.c
index 8445f7dcab..0ac6aebbbc 100644
--- a/config.c
+++ b/config.c
@@ -279,6 +279,11 @@ int git_default_config(const char *var, const char *value)
 		return 0;
 	}
 
+	if (!strcmp(var, "core.legacyheaders")) {
+		use_legacy_headers = git_config_bool(var, value);
+		return 0;
+	}
+
 	if (!strcmp(var, "core.compression")) {
 		int level = git_config_int(var, value);
 		if (level == -1)
diff --git a/config.mak.in b/config.mak.in
new file mode 100644
index 0000000000..04f508ab90
--- /dev/null
+++ b/config.mak.in
@@ -0,0 +1,24 @@
+# git Makefile configuration, included in main Makefile
+# @configure_input@
+
+CC = @CC@
+AR = @AR@
+TAR = @TAR@
+#INSTALL = @INSTALL@		# needs install-sh or install.sh in sources
+
+prefix = @prefix@
+exec_prefix = @exec_prefix@
+bindir = @bindir@
+#gitexecdir = @libexecdir@/git-core/
+datarootdir = @datarootdir@
+template_dir = @datadir@/git-core/templates/
+GIT_PYTHON_DIR = @datadir@/git-core/python
+
+mandir=@mandir@
+
+srcdir = @srcdir@
+VPATH = @srcdir@
+
+export exec_prefix mandir
+export srcdir VPATH
+
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000000..c1f7751e6f
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,183 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ(2.59)
+AC_INIT([git], [1.4.1], [git@vger.kernel.org])
+
+AC_CONFIG_SRCDIR([git.c])
+
+config_file=config.mak.autogen
+config_append=config.mak.append
+config_in=config.mak.in
+
+echo "# ${config_append}.  Generated by configure." > "${config_append}"
+
+
+## Definitions of macros
+# GIT_CONF_APPEND_LINE(LINE)
+# --------------------------
+# Append LINE to file ${config_append}
+AC_DEFUN([GIT_CONF_APPEND_LINE],
+[echo "$1" >> "${config_append}"])# GIT_CONF_APPEND_LINE
+
+
+## Checks for programs.
+AC_MSG_NOTICE([CHECKS for programs])
+#
+AC_PROG_CC
+#AC_PROG_INSTALL		# needs install-sh or install.sh in sources
+AC_CHECK_TOOL(AR, ar, :)
+AC_CHECK_PROGS(TAR, [gtar tar])
+#
+# Define NO_PYTHON if you want to lose all benefits of the recursive merge.
+
+
+## Checks for libraries.
+AC_MSG_NOTICE([CHECKS for libraries])
+#
+# Define NO_OPENSSL environment variable if you do not have OpenSSL.
+# Define NEEDS_SSL_WITH_CRYPTO if you need -lcrypto with -lssl (Darwin).
+AC_CHECK_LIB([ssl], [SHA1_Init],[],
+[AC_CHECK_LIB([crypto], [SHA1_INIT],
+ [GIT_CONF_APPEND_LINE(NEEDS_SSL_WITH_CRYPTO=YesPlease)],
+ [GIT_CONF_APPEND_LINE(NO_OPENSSL=YesPlease)])])
+#
+# Define NO_CURL if you do not have curl installed.  git-http-pull and
+# git-http-push are not built, and you cannot use http:// and https://
+# transports.
+AC_CHECK_LIB([curl], [curl_global_init],[],
+[GIT_CONF_APPEND_LINE(NO_CURL=YesPlease)])
+#
+# Define NO_EXPAT if you do not have expat installed.  git-http-push is
+# not built, and you cannot push using http:// and https:// transports.
+AC_CHECK_LIB([expat], [XML_ParserCreate],[],
+[GIT_CONF_APPEND_LINE(NO_EXPAT=YesPlease)])
+#
+# Define NEEDS_LIBICONV if linking with libc is not enough (Darwin).
+AC_CHECK_LIB([c], [iconv],[],
+[AC_CHECK_LIB([iconv],[iconv],
+ [GIT_CONF_APPEND_LINE(NEEDS_LIBICONV=YesPlease)],[])])
+#
+# Define NEEDS_SOCKET if linking with libc is not enough (SunOS,
+# Patrick Mauritz).
+AC_CHECK_LIB([c], [socket],[],
+[AC_CHECK_LIB([socket],[socket],
+ [GIT_CONF_APPEND_LINE(NEEDS_SOCKET=YesPlease)],[])])
+
+
+## Checks for header files.
+
+
+## Checks for typedefs, structures, and compiler characteristics.
+AC_MSG_NOTICE([CHECKS for typedefs, structures, and compiler characteristics])
+#
+# Define NO_D_INO_IN_DIRENT if you don't have d_ino in your struct dirent.
+AC_CHECK_MEMBER(struct dirent.d_ino,[],
+[GIT_CONF_APPEND_LINE(NO_D_INO_IN_DIRENT=YesPlease)],
+[#include <dirent.h>])
+#
+# Define NO_D_TYPE_IN_DIRENT if your platform defines DT_UNKNOWN but lacks
+# d_type in struct dirent (latest Cygwin -- will be fixed soonish).
+AC_CHECK_MEMBER(struct dirent.d_type,[],
+[GIT_CONF_APPEND_LINE(NO_D_TYPE_IN_DIRENT=YesPlease)],
+[#include <dirent.h>])
+#
+# Define NO_SOCKADDR_STORAGE if your platform does not have struct
+# sockaddr_storage.
+AC_CHECK_TYPE(struct sockaddr_storage,[],
+[GIT_CONF_APPEND_LINE(NO_SOCKADDR_STORAGE=YesPlease)],
+[#include <netinet/in.h>])
+
+
+## Checks for library functions.
+## (in default C library and libraries checked by AC_CHECK_LIB)
+AC_MSG_NOTICE([CHECKS for library functions])
+#
+# Define NO_STRCASESTR if you don't have strcasestr.
+AC_CHECK_FUNC(strcasestr,[],
+[GIT_CONF_APPEND_LINE(NO_STRCASESTR=YesPlease)])
+#
+# Define NO_STRLCPY if you don't have strlcpy.
+AC_CHECK_FUNC(strlcpy,[],
+[GIT_CONF_APPEND_LINE(NO_STRLCPY=YesPlease)])
+#
+# Define NO_SETENV if you don't have setenv in the C library.
+AC_CHECK_FUNC(setenv,[],
+[GIT_CONF_APPEND_LINE(NO_SETENV=YesPlease)])
+#
+# Define NO_MMAP if you want to avoid mmap.
+#
+# Define NO_IPV6 if you lack IPv6 support and getaddrinfo().
+#
+# Define NO_ICONV if your libc does not properly support iconv.
+
+
+## Other checks.
+# Define USE_PIC if you need the main git objects to be built with -fPIC
+# in order to build and link perl/Git.so.  x86-64 seems to need this.
+#
+# Define NO_SYMLINK_HEAD if you never want .git/HEAD to be a symbolic link.
+# Enable it on Windows.  By default, symrefs are still used.
+#
+# Define WITH_OWN_SUBPROCESS_PY if you want to use with python 2.3.
+#
+# Define NO_ACCURATE_DIFF if your diff program at least sometimes misses
+# a missing newline at the end of the file.
+
+
+## Site configuration
+## --with-PACKAGE[=ARG] and --without-PACKAGE
+# Define NO_SVN_TESTS if you want to skip time-consuming SVN interopability
+# tests.  These tests take up a significant amount of the total test time
+# but are not needed unless you plan to talk to SVN repos.
+#
+# Define MOZILLA_SHA1 environment variable when running make to make use of
+# a bundled SHA1 routine coming from Mozilla. It is GPL'd and should be fast
+# on non-x86 architectures (e.g. PowerPC), while the OpenSSL version (default
+# choice) has very fast version optimized for i586.
+#
+# Define PPC_SHA1 environment variable when running make to make use of
+# a bundled SHA1 routine optimized for PowerPC.
+#
+# Define ARM_SHA1 environment variable when running make to make use of
+# a bundled SHA1 routine optimized for ARM.
+#
+# Define NO_OPENSSL environment variable if you do not have OpenSSL.
+# This also implies MOZILLA_SHA1.
+#
+# Define NO_CURL if you do not have curl installed.  git-http-pull and
+# git-http-push are not built, and you cannot use http:// and https://
+# transports.
+#
+# Define CURLDIR=/foo/bar if your curl header and library files are in
+# /foo/bar/include and /foo/bar/lib directories.
+#
+# Define NO_EXPAT if you do not have expat installed.  git-http-push is
+# not built, and you cannot push using http:// and https:// transports.
+#
+# Define NO_MMAP if you want to avoid mmap.
+#
+# Define NO_PYTHON if you want to loose all benefits of the recursive merge.
+#
+## --enable-FEATURE[=ARG] and --disable-FEATURE
+# Define COLLISION_CHECK below if you believe that SHA1's
+# 1461501637330902918203684832716283019655932542976 hashes do not give you
+# sufficient guarantee that no collisions between objects will ever happen.
+#
+# Define USE_NSEC below if you want git to care about sub-second file mtimes
+# and ctimes. Note that you need recent glibc (at least 2.2.4) for this, and
+# it will BREAK YOUR LOCAL DIFFS! show-diff and anything using it will likely
+# randomly break unless your underlying filesystem supports those sub-second
+# times (my ext3 doesn't).
+#
+# Define USE_STDEV below if you want git to care about the underlying device
+# change being considered an inode change from the update-cache perspective.
+
+
+## Output files
+AC_CONFIG_FILES(["${config_file}":"${config_in}":"${config_append}"])
+AC_OUTPUT
+
+
+## Cleanup
+rm -f "${config_append}"
diff --git a/contrib/emacs/Makefile b/contrib/emacs/Makefile
index d3619db510..350846de90 100644
--- a/contrib/emacs/Makefile
+++ b/contrib/emacs/Makefile
@@ -3,9 +3,9 @@
 EMACS = emacs
 
 ELC = git.elc vc-git.elc
-INSTALL = install
+INSTALL ?= install
 INSTALL_ELC = $(INSTALL) -m 644
-prefix = $(HOME)
+prefix ?= $(HOME)
 emacsdir = $(prefix)/share/emacs/site-lisp
 
 all: $(ELC)
diff --git a/contrib/emacs/git.el b/contrib/emacs/git.el
index 34c995046d..68de9be0c7 100644
--- a/contrib/emacs/git.el
+++ b/contrib/emacs/git.el
@@ -55,7 +55,8 @@
 ;;;; ------------------------------------------------------------
 
 (defgroup git nil
-  "Git user interface")
+  "A user interface for the git versioning system."
+  :group 'tools)
 
 (defcustom git-committer-name nil
   "User name to use for commits.
@@ -83,6 +84,12 @@ then to `add-log-mailing-address' and then to `user-mail-address'."
   :group 'git
   :type 'boolean)
 
+(defcustom git-reuse-status-buffer t
+  "Whether `git-status' should try to reuse an existing buffer
+if there is already one that displays the same directory."
+  :group 'git
+  :type 'boolean)
+
 (defcustom git-per-dir-ignore-file ".gitignore"
   "Name of the per-directory ignore file."
   :group 'git
@@ -258,7 +265,7 @@ and returns the process output as a string."
     (set-buffer (find-file-noselect ignore-name))
     (goto-char (point-max))
     (unless (zerop (current-column)) (insert "\n"))
-    (insert name "\n")
+    (insert "/" name "\n")
     (sort-lines nil (point-min) (point-max))
     (save-buffer))
   (when created
@@ -584,6 +591,8 @@ and returns the process output as a string."
                             (condition-case nil (delete-file ".git/MERGE_HEAD") (error nil))
                             (with-current-buffer buffer (erase-buffer))
                             (git-set-files-state files 'uptodate)
+                            (when (file-directory-p ".git/rr-cache")
+                              (git-run-command nil nil "rerere"))
                             (git-refresh-files)
                             (git-refresh-ewoc-hf git-status)
                             (message "Committed %s." commit))
@@ -1001,12 +1010,28 @@ Commands:
   (set (make-local-variable 'list-buffers-directory) default-directory)
   (run-hooks 'git-status-mode-hook)))
 
+(defun git-find-status-buffer (dir)
+  "Find the git status buffer handling a specified directory."
+  (let ((list (buffer-list))
+        (fulldir (expand-file-name dir))
+        found)
+    (while (and list (not found))
+      (let ((buffer (car list)))
+        (with-current-buffer buffer
+          (when (and list-buffers-directory
+                     (string-equal fulldir (expand-file-name list-buffers-directory))
+                     (string-match "\\*git-status\\*$" (buffer-name buffer)))
+            (setq found buffer))))
+      (setq list (cdr list)))
+    found))
+
 (defun git-status (dir)
   "Entry point into git-status mode."
   (interactive "DSelect directory: ")
   (setq dir (git-get-top-dir dir))
   (if (file-directory-p (concat (file-name-as-directory dir) ".git"))
-      (let ((buffer (create-file-buffer (expand-file-name "*git-status*" dir))))
+      (let ((buffer (or (and git-reuse-status-buffer (git-find-status-buffer dir))
+                        (create-file-buffer (expand-file-name "*git-status*" dir)))))
         (switch-to-buffer buffer)
         (cd dir)
         (git-status-mode)
diff --git a/daemon.c b/daemon.c
index e4ec676301..810837f0c4 100644
--- a/daemon.c
+++ b/daemon.c
@@ -19,7 +19,7 @@ static const char daemon_usage[] =
 "git-daemon [--verbose] [--syslog] [--inetd | --port=n] [--export-all]\n"
 "           [--timeout=n] [--init-timeout=n] [--strict-paths]\n"
 "           [--base-path=path] [--user-path | --user-path=path]\n"
-"           [--reuseaddr] [directory...]";
+"           [--reuseaddr] [--detach] [--pid-file=file] [directory...]";
 
 /* List of acceptable pathname prefixes */
 static char **ok_paths = NULL;
diff --git a/diff.c b/diff.c
index 8b44756136..6a71376483 100644
--- a/diff.c
+++ b/diff.c
@@ -17,15 +17,6 @@ static int diff_detect_rename_default = 0;
 static int diff_rename_limit_default = -1;
 static int diff_use_color_default = 0;
 
-enum color_diff {
-	DIFF_RESET = 0,
-	DIFF_PLAIN = 1,
-	DIFF_METAINFO = 2,
-	DIFF_FRAGINFO = 3,
-	DIFF_FILE_OLD = 4,
-	DIFF_FILE_NEW = 5,
-};
-
 /* "\033[1;38;5;2xx;48;5;2xxm\0" is 23 bytes */
 static char diff_colors[][24] = {
 	"\033[m",	/* reset */
@@ -33,7 +24,8 @@ static char diff_colors[][24] = {
 	"\033[1m",	/* bold */
 	"\033[36m",	/* cyan */
 	"\033[31m",	/* red */
-	"\033[32m"	/* green */
+	"\033[32m",	/* green */
+	"\033[33m"	/* yellow */
 };
 
 static int parse_diff_color_slot(const char *var, int ofs)
@@ -48,6 +40,8 @@ static int parse_diff_color_slot(const char *var, int ofs)
 		return DIFF_FILE_OLD;
 	if (!strcasecmp(var+ofs, "new"))
 		return DIFF_FILE_NEW;
+	if (!strcasecmp(var+ofs, "commit"))
+		return DIFF_COMMIT;
 	die("bad config variable '%s'", var);
 }
 
@@ -370,7 +364,7 @@ struct emit_callback {
 	const char **label_path;
 };
 
-static inline const char *get_color(int diff_use_color, enum color_diff ix)
+const char *diff_get_color(int diff_use_color, enum color_diff ix)
 {
 	if (diff_use_color)
 		return diff_colors[ix];
@@ -381,8 +375,8 @@ static void fn_out_consume(void *priv, char *line, unsigned long len)
 {
 	int i;
 	struct emit_callback *ecbdata = priv;
-	const char *set = get_color(ecbdata->color_diff, DIFF_METAINFO);
-	const char *reset = get_color(ecbdata->color_diff, DIFF_RESET);
+	const char *set = diff_get_color(ecbdata->color_diff, DIFF_METAINFO);
+	const char *reset = diff_get_color(ecbdata->color_diff, DIFF_RESET);
 
 	if (ecbdata->label_path[0]) {
 		printf("%s--- %s%s\n", set, ecbdata->label_path[0], reset);
@@ -397,7 +391,7 @@ static void fn_out_consume(void *priv, char *line, unsigned long len)
 		;
 	if (2 <= i && i < len && line[i] == ' ') {
 		ecbdata->nparents = i - 1;
-		set = get_color(ecbdata->color_diff, DIFF_FRAGINFO);
+		set = diff_get_color(ecbdata->color_diff, DIFF_FRAGINFO);
 	}
 	else if (len < ecbdata->nparents)
 		set = reset;
@@ -410,7 +404,7 @@ static void fn_out_consume(void *priv, char *line, unsigned long len)
 			else if (line[i] == '+')
 				color = DIFF_FILE_NEW;
 		}
-		set = get_color(ecbdata->color_diff, color);
+		set = diff_get_color(ecbdata->color_diff, color);
 	}
 	if (len > 0 && line[len-1] == '\n')
 		len--;
@@ -767,8 +761,8 @@ static void builtin_diff(const char *name_a,
 	mmfile_t mf1, mf2;
 	const char *lbl[2];
 	char *a_one, *b_two;
-	const char *set = get_color(o->color_diff, DIFF_METAINFO);
-	const char *reset = get_color(o->color_diff, DIFF_RESET);
+	const char *set = diff_get_color(o->color_diff, DIFF_METAINFO);
+	const char *reset = diff_get_color(o->color_diff, DIFF_RESET);
 
 	a_one = quote_two("a/", name_a);
 	b_two = quote_two("b/", name_b);
diff --git a/diff.h b/diff.h
index a06f959938..2cced530fa 100644
--- a/diff.h
+++ b/diff.h
@@ -69,6 +69,17 @@ struct diff_options {
 	add_remove_fn_t add_remove;
 };
 
+enum color_diff {
+	DIFF_RESET = 0,
+	DIFF_PLAIN = 1,
+	DIFF_METAINFO = 2,
+	DIFF_FRAGINFO = 3,
+	DIFF_FILE_OLD = 4,
+	DIFF_FILE_NEW = 5,
+	DIFF_COMMIT = 6,
+};
+const char *diff_get_color(int diff_use_color, enum color_diff ix);
+
 extern const char mime_boundary_leader[];
 
 extern void diff_tree_setup_paths(const char **paths, struct diff_options *);
diff --git a/environment.c b/environment.c
index 97d42b172b..42f39d657e 100644
--- a/environment.c
+++ b/environment.c
@@ -11,6 +11,7 @@
 
 char git_default_email[MAX_GITNAME];
 char git_default_name[MAX_GITNAME];
+int use_legacy_headers = 1;
 int trust_executable_bit = 1;
 int assume_unchanged = 0;
 int prefer_symlink_refs = 0;
diff --git a/fetch.c b/fetch.c
index 989d7a4788..aeb6bf2639 100644
--- a/fetch.c
+++ b/fetch.c
@@ -7,9 +7,7 @@
 #include "tag.h"
 #include "blob.h"
 #include "refs.h"
-
-const char *write_ref = NULL;
-const char *write_ref_log_details = NULL;
+#include "strbuf.h"
 
 int get_tree = 0;
 int get_history = 0;
@@ -213,54 +211,106 @@ static int mark_complete(const char *path, const unsigned char *sha1)
 	return 0;
 }
 
-int pull(char *target)
+int pull_targets_stdin(char ***target, const char ***write_ref)
+{
+	int targets = 0, targets_alloc = 0;
+	struct strbuf buf;
+	*target = NULL; *write_ref = NULL;
+	strbuf_init(&buf);
+	while (1) {
+		char *rf_one = NULL;
+		char *tg_one;
+
+		read_line(&buf, stdin, '\n');
+		if (buf.eof)
+			break;
+		tg_one = buf.buf;
+		rf_one = strchr(tg_one, '\t');
+		if (rf_one)
+			*rf_one++ = 0;
+
+		if (targets >= targets_alloc) {
+			targets_alloc = targets_alloc ? targets_alloc * 2 : 64;
+			*target = xrealloc(*target, targets_alloc * sizeof(**target));
+			*write_ref = xrealloc(*write_ref, targets_alloc * sizeof(**write_ref));
+		}
+		(*target)[targets] = strdup(tg_one);
+		(*write_ref)[targets] = rf_one ? strdup(rf_one) : NULL;
+		targets++;
+	}
+	return targets;
+}
+
+void pull_targets_free(int targets, char **target, const char **write_ref)
 {
-	struct ref_lock *lock = NULL;
-	unsigned char sha1[20];
+	while (targets--) {
+		free(target[targets]);
+		if (write_ref && write_ref[targets])
+			free((char *) write_ref[targets]);
+	}
+}
+
+int pull(int targets, char **target, const char **write_ref,
+         const char *write_ref_log_details)
+{
+	struct ref_lock **lock = xcalloc(targets, sizeof(struct ref_lock *));
+	unsigned char *sha1 = xmalloc(targets * 20);
 	char *msg;
 	int ret;
+	int i;
 
 	save_commit_buffer = 0;
 	track_object_refs = 0;
-	if (write_ref) {
-		lock = lock_ref_sha1(write_ref, NULL, 0);
-		if (!lock) {
-			error("Can't lock ref %s", write_ref);
-			return -1;
+
+	for (i = 0; i < targets; i++) {
+		if (!write_ref || !write_ref[i])
+			continue;
+
+		lock[i] = lock_ref_sha1(write_ref[i], NULL, 0);
+		if (!lock[i]) {
+			error("Can't lock ref %s", write_ref[i]);
+			goto unlock_and_fail;
 		}
 	}
 
 	if (!get_recover)
 		for_each_ref(mark_complete);
 
-	if (interpret_target(target, sha1)) {
-		error("Could not interpret %s as something to pull", target);
-		if (lock)
-			unlock_ref(lock);
-		return -1;
+	for (i = 0; i < targets; i++) {
+		if (interpret_target(target[i], &sha1[20 * i])) {
+			error("Could not interpret %s as something to pull", target[i]);
+			goto unlock_and_fail;
+		}
+		if (process(lookup_unknown_object(&sha1[20 * i])))
+			goto unlock_and_fail;
 	}
-	if (process(lookup_unknown_object(sha1))) {
-		if (lock)
-			unlock_ref(lock);
-		return -1;
+
+	if (loop())
+		goto unlock_and_fail;
+
+	if (write_ref_log_details) {
+		msg = xmalloc(strlen(write_ref_log_details) + 12);
+		sprintf(msg, "fetch from %s", write_ref_log_details);
+	} else {
+		msg = NULL;
 	}
-	if (loop()) {
-		if (lock)
-			unlock_ref(lock);
-		return -1;
+	for (i = 0; i < targets; i++) {
+		if (!write_ref || !write_ref[i])
+			continue;
+		ret = write_ref_sha1(lock[i], &sha1[20 * i], msg ? msg : "fetch (unknown)");
+		lock[i] = NULL;
+		if (ret)
+			goto unlock_and_fail;
 	}
+	if (msg)
+		free(msg);
 
-	if (write_ref) {
-		if (write_ref_log_details) {
-			msg = xmalloc(strlen(write_ref_log_details) + 12);
-			sprintf(msg, "fetch from %s", write_ref_log_details);
-		}
-		else
-			msg = NULL;
-		ret = write_ref_sha1(lock, sha1, msg ? msg : "fetch (unknown)");
-		if (msg)
-			free(msg);
-		return ret;
-	}
 	return 0;
+
+
+unlock_and_fail:
+	for (i = 0; i < targets; i++)
+		if (lock[i])
+			unlock_ref(lock[i]);
+	return -1;
 }
diff --git a/fetch.h b/fetch.h
index 841bb1af9c..be48c6f190 100644
--- a/fetch.h
+++ b/fetch.h
@@ -22,12 +22,6 @@ extern void prefetch(unsigned char *sha1);
  */
 extern int fetch_ref(char *ref, unsigned char *sha1);
 
-/* If set, the ref filename to write the target value to. */
-extern const char *write_ref;
-
-/* If set additional text will appear in the ref log. */
-extern const char *write_ref_log_details;
-
 /* Set to fetch the target tree. */
 extern int get_tree;
 
@@ -46,6 +40,15 @@ extern int get_recover;
 /* Report what we got under get_verbosely */
 extern void pull_say(const char *, const char *);
 
-extern int pull(char *target);
+/* Load pull targets from stdin */
+extern int pull_targets_stdin(char ***target, const char ***write_ref);
+
+/* Free up loaded targets */
+extern void pull_targets_free(int targets, char **target, const char **write_ref);
+
+/* If write_ref is set, the ref filename to write the target value to. */
+/* If write_ref_log_details is set, additional text will appear in the ref log. */
+extern int pull(int targets, char **target, const char **write_ref,
+		const char *write_ref_log_details);
 
 #endif /* PULL_H */
diff --git a/git-am.sh b/git-am.sh
index db9a20a811..04f0119435 100755
--- a/git-am.sh
+++ b/git-am.sh
@@ -91,6 +91,7 @@ fall_back_3way () {
 }
 
 prec=4
+rloga=am
 dotest=.dotest sign= utf8= keep= skip= interactive= resolved= binary= ws= resolvemsg=
 
 while case "$#" in 0) break;; esac
@@ -130,6 +131,9 @@ do
 	--resolvemsg=*)
 	resolvemsg=$(echo "$1" | sed -e "s/^--resolvemsg=//"); shift ;;
 
+	--reflog-action=*)
+	rloga=`expr "z$1" : 'z-[^=]*=\(.*\)'`; shift ;;
+
 	--)
 	shift; break ;;
 	-*)
@@ -152,8 +156,10 @@ fi
 
 if test -d "$dotest"
 then
-	test ",$#," = ",0," ||
-	die "previous dotest directory $dotest still exists but mbox given."
+	if test ",$#," != ",0," || ! tty -s
+	then
+		die "previous dotest directory $dotest still exists but mbox given."
+	fi
 	resume=yes
 else
 	# Make sure we are not given --skip nor --resolved
@@ -413,7 +419,7 @@ do
 	parent=$(git-rev-parse --verify HEAD) &&
 	commit=$(git-commit-tree $tree -p $parent <"$dotest/final-commit") &&
 	echo Committed: $commit &&
-	git-update-ref -m "am: $SUBJECT" HEAD $commit $parent ||
+	git-update-ref -m "$rloga: $SUBJECT" HEAD $commit $parent ||
 	stop_here $this
 
 	if test -x "$GIT_DIR"/hooks/post-applypatch
diff --git a/git-clone.sh b/git-clone.sh
index 0368803883..a92b22a13d 100755
--- a/git-clone.sh
+++ b/git-clone.sh
@@ -266,7 +266,7 @@ yes,yes)
 	    echo "$repo/objects" >> "$GIT_DIR/objects/info/alternates"
 	    ;;
 	esac
-	git-ls-remote "$repo" >"$GIT_DIR/CLONE_HEAD"
+	git-ls-remote "$repo" >"$GIT_DIR/CLONE_HEAD" || exit 1
 	;;
 *)
 	case "$repo" in
@@ -296,7 +296,7 @@ yes,yes)
 		    done
 		    rm -f "$GIT_DIR/TMP_ALT"
 		fi
-		git-ls-remote "$repo" >"$GIT_DIR/CLONE_HEAD"
+		git-ls-remote "$repo" >"$GIT_DIR/CLONE_HEAD" || exit 1
 		;;
 	http://*)
 		if test -z "@@NO_CURL@@"
diff --git a/git-cvsexportcommit.perl b/git-cvsexportcommit.perl
index 5d13a54194..99b3dc392a 100755
--- a/git-cvsexportcommit.perl
+++ b/git-cvsexportcommit.perl
@@ -16,9 +16,9 @@ unless ($ENV{GIT_DIR} && -r $ENV{GIT_DIR}){
     die "GIT_DIR is not defined or is unreadable";
 }
 
-our ($opt_h, $opt_p, $opt_v, $opt_c, $opt_f, $opt_m );
+our ($opt_h, $opt_p, $opt_v, $opt_c, $opt_f, $opt_a, $opt_m );
 
-getopts('hpvcfm:');
+getopts('hpvcfam:');
 
 $opt_h && usage();
 
@@ -29,7 +29,6 @@ our ($tmpdir, $tmpdirname) = tempdir('git-cvsapplycommit-XXXXXX',
 				     TMPDIR => 1,
 				     CLEANUP => 1);
 
-print Dumper(@ARGV);
 # resolve target commit
 my $commit;
 $commit = pop @ARGV;
@@ -53,12 +52,32 @@ if (@ARGV) {
 # find parents from the commit itself
 my @commit  = safe_pipe_capture('git-cat-file', 'commit', $commit);
 my @parents;
-foreach my $p (@commit) {
-    if ($p =~ m/^$/) { # end of commit headers, we're done
-	last;
+my $committer;
+my $author;
+my $stage = 'headers'; # headers, msg
+my $title;
+my $msg = '';
+
+foreach my $line (@commit) {
+    chomp $line;
+    if ($stage eq 'headers' && $line eq '') {
+	$stage = 'msg';
+	next;
     }
-    if ($p =~ m/^parent (\w{40})$/) { # found a parent
-	push @parents, $1;
+
+    if ($stage eq 'headers') {
+	if ($line =~ m/^parent (\w{40})$/) { # found a parent
+	    push @parents, $1;
+	} elsif ($line =~ m/^author (.+) \d+ \+\d+$/) {
+	    $author = $1;
+	} elsif ($line =~ m/^committer (.+) \d+ \+\d+$/) {
+	    $committer = $1;
+	}
+    } else {
+	$msg .= $line . "\n";
+	unless ($title) {
+	    $title = $line;
+	}
     }
 }
 
@@ -84,12 +103,18 @@ $opt_v && print "Applying to CVS commit $commit from parent $parent\n";
 
 # grab the commit message
 open(MSG, ">.msg") or die "Cannot open .msg for writing";
-print MSG $opt_m;
+if ($opt_m) {
+    print MSG $opt_m;
+}
+print MSG $msg;
+if ($opt_a) {
+    print MSG "\n\nAuthor: $author\n";
+    if ($author ne $committer) {
+	print MSG "Committer: $committer\n";
+    }
+}
 close MSG;
 
-`git-cat-file commit $commit | sed -e '1,/^\$/d' >> .msg`;
-$? && die "Error extracting the commit message";
-
 my (@afiles, @dfiles, @mfiles, @dirs);
 my @files = safe_pipe_capture('git-diff-tree', '-r', $parent, $commit);
 #print @files;
@@ -233,6 +258,7 @@ foreach my $f (@dfiles) {
 }
 
 print "Commit to CVS\n";
+print "Patch: $title\n";
 my $commitfiles = join(' ', @afiles, @mfiles, @dfiles);
 my $cmd = "cvs commit -F .msg $commitfiles";
 
diff --git a/git-cvsserver.perl b/git-cvsserver.perl
index c30ef70427..2130d57020 100755
--- a/git-cvsserver.perl
+++ b/git-cvsserver.perl
@@ -81,7 +81,7 @@ my $methods = {
 
 # $state holds all the bits of information the clients sends us that could
 # potentially be useful when it comes to actually _doing_ something.
-my $state = {};
+my $state = { prependdir => '' };
 $log->info("--------------- STARTING -----------------");
 
 my $TEMP_DIR = tempdir( CLEANUP => 1 );
@@ -547,12 +547,15 @@ sub req_Argument
 {
     my ( $cmd, $data ) = @_;
 
-    # TODO :  Not quite sure how Argument and Argumentx differ, but I assume
-    # it's for multi-line arguments ... somehow ...
+    # Argumentx means: append to last Argument (with a newline in front)
 
     $log->debug("$cmd : $data");
 
-    push @{$state->{arguments}}, $data;
+    if ( $cmd eq 'Argumentx') {
+        ${$state->{arguments}}[$#{$state->{arguments}}] .= "\n" . $data;
+    } else {
+        push @{$state->{arguments}}, $data;
+    }
 }
 
 # expand-modules \n
@@ -1139,9 +1142,7 @@ sub req_ci
         exit;
     }
 
-    open FILE, ">", "$ENV{GIT_DIR}refs/heads/$state->{module}";
-    print FILE $commithash;
-    close FILE;
+    print LOCKFILE $commithash;
 
     $updater->update();
 
@@ -1168,7 +1169,9 @@ sub req_ci
     }
 
     close LOCKFILE;
-    unlink($lockfile);
+    my $reffile = "$ENV{GIT_DIR}refs/heads/$state->{module}";
+    unlink($reffile);
+    rename($lockfile, $reffile);
     chdir "/";
 
     print "ok\n";
@@ -2129,12 +2132,6 @@ sub update
     # first lets get the commit list
     $ENV{GIT_DIR} = $self->{git_path};
 
-    # prepare database queries
-    my $db_insert_rev = $self->{dbh}->prepare_cached("INSERT INTO revision (name, revision, filehash, commithash, modified, author, mode) VALUES (?,?,?,?,?,?,?)",{},1);
-    my $db_insert_mergelog = $self->{dbh}->prepare_cached("INSERT INTO commitmsgs (key, value) VALUES (?,?)",{},1);
-    my $db_delete_head = $self->{dbh}->prepare_cached("DELETE FROM head",{},1);
-    my $db_insert_head = $self->{dbh}->prepare_cached("INSERT INTO head (name, revision, filehash, commithash, modified, author, mode) VALUES (?,?,?,?,?,?,?)",{},1);
-
     my $commitinfo = `git-cat-file commit $self->{module} 2>&1`;
     unless ( $commitinfo =~ /tree\s+[a-zA-Z0-9]{40}/ )
     {
@@ -2323,7 +2320,7 @@ sub update
                         author => $commit->{author},
                         mode => $git_perms,
                     };
-                    $db_insert_rev->execute($4, $head->{$4}{revision}, $2, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
+                    $self->insert_rev($4, $head->{$4}{revision}, $2, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
                 }
                 elsif ( $3 eq "M" )
                 {
@@ -2337,7 +2334,7 @@ sub update
                         author => $commit->{author},
                         mode => $git_perms,
                     };
-                    $db_insert_rev->execute($4, $head->{$4}{revision}, $2, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
+                    $self->insert_rev($4, $head->{$4}{revision}, $2, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
                 }
                 elsif ( $3 eq "A" )
                 {
@@ -2351,7 +2348,7 @@ sub update
                         author => $commit->{author},
                         mode => $git_perms,
                     };
-                    $db_insert_rev->execute($4, $head->{$4}{revision}, $2, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
+                    $self->insert_rev($4, $head->{$4}{revision}, $2, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
                 }
                 else
                 {
@@ -2408,7 +2405,7 @@ sub update
                     };
 
 
-                    $db_insert_rev->execute($git_filename, $newrevision, $git_hash, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
+                    $self->insert_rev($git_filename, $newrevision, $git_hash, $commit->{hash}, $commit->{date}, $commit->{author}, $git_perms);
                 }
             }
             close FILELIST;
@@ -2424,7 +2421,7 @@ sub update
                     $head->{$file}{modified} = $commit->{date};
                     $head->{$file}{author} = $commit->{author};
 
-                    $db_insert_rev->execute($file, $head->{$file}{revision}, $head->{$file}{filehash}, $commit->{hash}, $commit->{date}, $commit->{author}, $head->{$file}{mode});
+                    $self->insert_rev($file, $head->{$file}{revision}, $head->{$file}{filehash}, $commit->{hash}, $commit->{date}, $commit->{author}, $head->{$file}{mode});
                 }
             }
             # END : "Detect deleted files"
@@ -2433,7 +2430,7 @@ sub update
 
         if (exists $commit->{mergemsg})
         {
-            $db_insert_mergelog->execute($commit->{hash}, $commit->{mergemsg});
+            $self->insert_mergelog($commit->{hash}, $commit->{mergemsg});
         }
 
         $lastpicked = $commit->{hash};
@@ -2441,10 +2438,10 @@ sub update
         $self->_set_prop("last_commit", $commit->{hash});
     }
 
-    $db_delete_head->execute();
+    $self->delete_head();
     foreach my $file ( keys %$head )
     {
-        $db_insert_head->execute(
+        $self->insert_head(
             $file,
             $head->{$file}{revision},
             $head->{$file}{filehash},
@@ -2462,6 +2459,54 @@ sub update
     $self->{dbh}->commit() or die "Failed to commit changes to SQLite";
 }
 
+sub insert_rev
+{
+    my $self = shift;
+    my $name = shift;
+    my $revision = shift;
+    my $filehash = shift;
+    my $commithash = shift;
+    my $modified = shift;
+    my $author = shift;
+    my $mode = shift;
+
+    my $insert_rev = $self->{dbh}->prepare_cached("INSERT INTO revision (name, revision, filehash, commithash, modified, author, mode) VALUES (?,?,?,?,?,?,?)",{},1);
+    $insert_rev->execute($name, $revision, $filehash, $commithash, $modified, $author, $mode);
+}
+
+sub insert_mergelog
+{
+    my $self = shift;
+    my $key = shift;
+    my $value = shift;
+
+    my $insert_mergelog = $self->{dbh}->prepare_cached("INSERT INTO commitmsgs (key, value) VALUES (?,?)",{},1);
+    $insert_mergelog->execute($key, $value);
+}
+
+sub delete_head
+{
+    my $self = shift;
+
+    my $delete_head = $self->{dbh}->prepare_cached("DELETE FROM head",{},1);
+    $delete_head->execute();
+}
+
+sub insert_head
+{
+    my $self = shift;
+    my $name = shift;
+    my $revision = shift;
+    my $filehash = shift;
+    my $commithash = shift;
+    my $modified = shift;
+    my $author = shift;
+    my $mode = shift;
+
+    my $insert_head = $self->{dbh}->prepare_cached("INSERT INTO head (name, revision, filehash, commithash, modified, author, mode) VALUES (?,?,?,?,?,?,?)",{},1);
+    $insert_head->execute($name, $revision, $filehash, $commithash, $modified, $author, $mode);
+}
+
 sub _headrev
 {
     my $self = shift;
diff --git a/git-fetch.sh b/git-fetch.sh
index ff1769952b..c2eebee798 100755
--- a/git-fetch.sh
+++ b/git-fetch.sh
@@ -20,6 +20,7 @@ verbose=
 update_head_ok=
 exec=
 upload_pack=
+keep=--thin
 while case "$#" in 0) break ;; esac
 do
 	case "$1" in
@@ -69,7 +70,8 @@ case "$#" in
 0)
 	test -f "$GIT_DIR/branches/origin" ||
 		test -f "$GIT_DIR/remotes/origin" ||
-			die "Where do you want to fetch from today?"
+			git-repo-config --get remote.origin.url >/dev/null ||
+				die "Where do you want to fetch from today?"
 	set origin ;;
 esac
 
@@ -153,7 +155,7 @@ fast_forward_local () {
 	then
 		if now_=$(cat "$GIT_DIR/$1") && test "$now_" = "$2"
 		then
-			[ "$verbose" ] && echo >&2 "* $1: same as $3"
+			[ "$verbose" ] && echo >&2 "* $1: same as $3" ||:
 		else
 			echo >&2 "* $1: updating with $3"
 			git-update-ref -m "$rloga: updating tag" "$1" "$2"
@@ -223,9 +225,16 @@ reflist=$(get_remote_refs_for_fetch "$@")
 if test "$tags"
 then
 	taglist=`IFS="	" &&
-		  git-ls-remote $upload_pack --tags "$remote" |
+		  (
+			git-ls-remote $upload_pack --tags "$remote" ||
+			echo fail ouch
+		  ) |
 	          while read sha1 name
 		  do
+			case "$sha1" in
+			fail)
+				exit 1
+			esac
 			case "$name" in
 			*^*) continue ;;
 			esac
@@ -235,7 +244,7 @@ then
 			else
 			    echo >&2 "warning: tag ${name} ignored"
 			fi
-		  done`
+		  done` || exit
 	if test "$#" -gt 1
 	then
 		# remote URL plus explicit refspecs; we need to merge them.
@@ -347,7 +356,7 @@ fetch_main () {
     ( : subshell because we muck with IFS
       IFS=" 	$LF"
       (
-	  git-fetch-pack $exec $keep --thin "$remote" $rref || echo failed "$remote"
+	  git-fetch-pack $exec $keep "$remote" $rref || echo failed "$remote"
       ) |
       while read sha1 remote_name
       do
diff --git a/git-instaweb.sh b/git-instaweb.sh
index 63b18b99f6..16cd351f7f 100755
--- a/git-instaweb.sh
+++ b/git-instaweb.sh
@@ -54,6 +54,10 @@ start_httpd () {
 			fi
 		done
 	fi
+	if test $? != 0; then
+		echo "Could not execute http daemon $httpd."
+		exit 1
+	fi
 }
 
 stop_httpd () {
@@ -183,8 +187,10 @@ PerlPassEnv GIT_EXEC_DIR
 EOF
 	else
 		# plain-old CGI
+		list_mods=`echo "$httpd" | sed "s/-f$/-l/"`
+		$list_mods | grep 'mod_cgi\.c' >/dev/null 2>&1 || \
+		echo "LoadModule cgi_module $module_path/mod_cgi.so" >> "$conf"
 		cat >> "$conf" <<EOF
-LoadModule cgi_module $module_path/mod_cgi.so
 AddHandler cgi-script .cgi
 <Location /gitweb.cgi>
 	Options +ExecCGI
@@ -232,4 +238,5 @@ esac
 
 start_httpd
 test -z "$browser" && browser=echo
-$browser http://127.0.0.1:$port
+url=http://127.0.0.1:$port
+$browser $url || echo $url
diff --git a/git-lost-found.sh b/git-lost-found.sh
index ba6d587f31..b928f2ca52 100755
--- a/git-lost-found.sh
+++ b/git-lost-found.sh
@@ -12,7 +12,7 @@ fi
 laf="$GIT_DIR/lost-found"
 rm -fr "$laf" && mkdir -p "$laf/commit" "$laf/other" || exit
 
-git fsck-objects |
+git fsck-objects --full |
 while read dangling type sha1
 do
 	case "$dangling" in
diff --git a/git-merge.sh b/git-merge.sh
index 9b681159dc..d049e16431 100755
--- a/git-merge.sh
+++ b/git-merge.sh
@@ -63,7 +63,13 @@ squash_message () {
 }
 
 finish () {
-	test '' = "$2" || echo "$2"
+	if test '' = "$2"
+	then
+		rlogm="$rloga"
+	else
+		echo "$2"
+		rlogm="$rloga: $2"
+	fi
 	case "$squash" in
 	t)
 		echo "Squash commit -- not updating HEAD"
@@ -75,7 +81,7 @@ finish () {
 			echo "No merge message -- not updating HEAD"
 			;;
 		*)
-			git-update-ref HEAD "$1" "$head" || exit 1
+			git-update-ref -m "$rlogm" HEAD "$1" "$head" || exit 1
 			;;
 		esac
 		;;
@@ -93,6 +99,7 @@ finish () {
 	esac
 }
 
+rloga=
 while case "$#" in 0) break ;; esac
 do
 	case "$1" in
@@ -126,6 +133,9 @@ do
 			die "available strategies are: $all_strategies" ;;
 		esac
 		;;
+	--reflog-action=*)
+		rloga=`expr "z$1" : 'z-[^=]*=\(.*\)'`
+		;;
 	-*)	usage ;;
 	*)	break ;;
 	esac
@@ -140,6 +150,7 @@ shift
 
 # All the rest are remote heads
 test "$#" = 0 && usage ;# we need at least one remote head.
+test "$rloga" = '' && rloga="merge: $@"
 
 remoteheads=
 for remote
@@ -325,7 +336,7 @@ if test '' != "$result_tree"
 then
     parents=$(git-show-branch --independent "$head" "$@" | sed -e 's/^/-p /')
     result_commit=$(echo "$merge_msg" | git-commit-tree $result_tree $parents) || exit
-    finish "$result_commit" "Merge $result_commit, made by $wt_strategy."
+    finish "$result_commit" "Merge made by $wt_strategy."
     dropsave
     exit 0
 fi
diff --git a/git-mv.perl b/git-mv.perl
deleted file mode 100755
index 75aa8feeb6..0000000000
--- a/git-mv.perl
+++ /dev/null
@@ -1,250 +0,0 @@
-#!/usr/bin/perl
-#
-# Copyright 2005, Ryan Anderson <ryan@michonline.com>
-#                 Josef Weidendorfer <Josef.Weidendorfer@gmx.de>
-#
-# This file is licensed under the GPL v2, or a later version
-# at the discretion of Linus Torvalds.
-
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-sub usage() {
-	print <<EOT;
-$0 [-f] [-n] <source> <destination>
-$0 [-f] [-n] [-k] <source> ... <destination directory>
-EOT
-	exit(1);
-}
-
-our ($opt_n, $opt_f, $opt_h, $opt_k, $opt_v);
-getopts("hnfkv") || usage;
-usage() if $opt_h;
-@ARGV >= 1 or usage;
-
-my $GIT_DIR = `git rev-parse --git-dir`;
-exit 1 if $?; # rev-parse would have given "not a git dir" message.
-chomp($GIT_DIR);
-
-my (@srcArgs, @dstArgs, @srcs, @dsts);
-my ($src, $dst, $base, $dstDir);
-
-# remove any trailing slash in arguments
-for (@ARGV) { s/\/*$//; }
-
-my $argCount = scalar @ARGV;
-if (-d $ARGV[$argCount-1]) {
-	$dstDir = $ARGV[$argCount-1];
-	@srcArgs = @ARGV[0..$argCount-2];
-
-	foreach $src (@srcArgs) {
-		$base = $src;
-		$base =~ s/^.*\///;
-		$dst = "$dstDir/". $base;
-		push @dstArgs, $dst;
-	}
-}
-else {
-    if ($argCount < 2) {
-	print "Error: need at least two arguments\n";
-	exit(1);
-    }
-    if ($argCount > 2) {
-	print "Error: moving to directory '"
-	    . $ARGV[$argCount-1]
-	    . "' not possible; not existing\n";
-	exit(1);
-    }
-    @srcArgs = ($ARGV[0]);
-    @dstArgs = ($ARGV[1]);
-    $dstDir = "";
-}
-
-my $subdir_prefix = `git rev-parse --show-prefix`;
-chomp($subdir_prefix);
-
-# run in git base directory, so that git-ls-files lists all revisioned files
-chdir "$GIT_DIR/..";
-
-# normalize paths, needed to compare against versioned files and update-index
-# also, this is nicer to end-users by doing ".//a/./b/.//./c" ==> "a/b/c"
-for (@srcArgs, @dstArgs) {
-    # prepend git prefix as we run from base directory
-    $_ = $subdir_prefix.$_;
-    s|^\./||;
-    s|/\./|/| while (m|/\./|);
-    s|//+|/|g;
-    # Also "a/b/../c" ==> "a/c"
-    1 while (s,(^|/)[^/]+/\.\./,$1,);
-}
-
-my (@allfiles,@srcfiles,@dstfiles);
-my $safesrc;
-my (%overwritten, %srcForDst);
-
-$/ = "\0";
-open(F, 'git-ls-files -z |')
-        or die "Failed to open pipe from git-ls-files: " . $!;
-
-@allfiles = map { chomp; $_; } <F>;
-close(F);
-
-
-my ($i, $bad);
-while(scalar @srcArgs > 0) {
-    $src = shift @srcArgs;
-    $dst = shift @dstArgs;
-    $bad = "";
-
-    for ($src, $dst) {
-	# Be nicer to end-users by doing ".//a/./b/.//./c" ==> "a/b/c"
-	s|^\./||;
-	s|/\./|/| while (m|/\./|);
-	s|//+|/|g;
-	# Also "a/b/../c" ==> "a/c"
-	1 while (s,(^|/)[^/]+/\.\./,$1,);
-    }
-
-    if ($opt_v) {
-	print "Checking rename of '$src' to '$dst'\n";
-    }
-
-    unless (-f $src || -l $src || -d $src) {
-	$bad = "bad source '$src'";
-    }
-
-    $safesrc = quotemeta($src);
-    @srcfiles = grep /^$safesrc(\/|$)/, @allfiles;
-
-    $overwritten{$dst} = 0;
-    if (($bad eq "") && -e $dst) {
-	$bad = "destination '$dst' already exists";
-	if ($opt_f) {
-	    # only files can overwrite each other: check both source and destination
-	    if (-f $dst && (scalar @srcfiles == 1)) {
-		print "Warning: $bad; will overwrite!\n";
-		$bad = "";
-		$overwritten{$dst} = 1;
-	    }
-	    else {
-		$bad = "Can not overwrite '$src' with '$dst'";
-	    }
-	}
-    }
-    
-    if (($bad eq "") && ($dst =~ /^$safesrc\//)) {
-	$bad = "can not move directory '$src' into itself";
-    }
-
-    if ($bad eq "") {
-        if (scalar @srcfiles == 0) {
-	    $bad = "'$src' not under version control";
-	}
-    }
-
-    if ($bad eq "") {
-       if (defined $srcForDst{$dst}) {
-           $bad = "can not move '$src' to '$dst'; already target of ";
-           $bad .= "'".$srcForDst{$dst}."'";
-       }
-       else {
-           $srcForDst{$dst} = $src;
-       }
-    }
-
-    if ($bad ne "") {
-	if ($opt_k) {
-	    print "Warning: $bad; skipping\n";
-	    next;
-	}
-	print "Error: $bad\n";
-	exit(1);
-    }
-    push @srcs, $src;
-    push @dsts, $dst;
-}
-
-# Final pass: rename/move
-my (@deletedfiles,@addedfiles,@changedfiles);
-$bad = "";
-while(scalar @srcs > 0) {
-    $src = shift @srcs;
-    $dst = shift @dsts;
-
-    if ($opt_n || $opt_v) { print "Renaming $src to $dst\n"; }
-    if (!$opt_n) {
-	if (!rename($src,$dst)) {
-	    $bad = "renaming '$src' failed: $!";
-	    if ($opt_k) {
-		print "Warning: skipped: $bad\n";
-		$bad = "";
-		next;
-	    }
-	    last;
-	}
-    }
-
-    $safesrc = quotemeta($src);
-    @srcfiles = grep /^$safesrc(\/|$)/, @allfiles;
-    @dstfiles = @srcfiles;
-    s/^$safesrc(\/|$)/$dst$1/ for @dstfiles;
-
-    push @deletedfiles, @srcfiles;
-    if (scalar @srcfiles == 1) {
-	# $dst can be a directory with 1 file inside
-	if ($overwritten{$dst} ==1) {
-	    push @changedfiles, $dstfiles[0];
-
-	} else {
-	    push @addedfiles, $dstfiles[0];
-	}
-    }
-    else {
-	push @addedfiles, @dstfiles;
-    }
-}
-
-if ($opt_n) {
-    if (@changedfiles) {
-	print "Changed  : ". join(", ", @changedfiles) ."\n";
-    }
-    if (@addedfiles) {
-	print "Adding   : ". join(", ", @addedfiles) ."\n";
-    }
-    if (@deletedfiles) {
-	print "Deleting : ". join(", ", @deletedfiles) ."\n";
-    }
-}
-else {
-    if (@changedfiles) {
-	open(H, "| git-update-index -z --stdin")
-		or die "git-update-index failed to update changed files with code $!\n";
-	foreach my $fileName (@changedfiles) {
-		print H "$fileName\0";
-	}
-	close(H);
-    }
-    if (@addedfiles) {
-	open(H, "| git-update-index --add -z --stdin")
-		or die "git-update-index failed to add new names with code $!\n";
-	foreach my $fileName (@addedfiles) {
-		print H "$fileName\0";
-	}
-	close(H);
-    }
-    if (@deletedfiles) {
-	open(H, "| git-update-index --remove -z --stdin")
-		or die "git-update-index failed to remove old names with code $!\n";
-	foreach my $fileName (@deletedfiles) {
-		print H "$fileName\0";
-	}
-	close(H);
-    }
-}
-
-if ($bad ne "") {
-    print "Error: $bad\n";
-    exit(1);
-}
diff --git a/git-pull.sh b/git-pull.sh
index d337bf4da3..f380437997 100755
--- a/git-pull.sh
+++ b/git-pull.sh
@@ -102,5 +102,6 @@ case "$strategy_args" in
 esac
 
 merge_name=$(git-fmt-merge-msg <"$GIT_DIR/FETCH_HEAD") || exit
-git-merge $no_summary $no_commit $squash $strategy_args \
+git-merge "--reflog-action=pull $*" \
+	$no_summary $no_commit $squash $strategy_args \
 	"$merge_name" HEAD $merge_head
diff --git a/git-quiltimport.sh b/git-quiltimport.sh
index 364baff806..10135da3ac 100755
--- a/git-quiltimport.sh
+++ b/git-quiltimport.sh
@@ -112,7 +112,7 @@ for patch_name in $(cat "$QUILT_PATCHES/series" | grep -v '^#'); do
 		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
+		git-update-ref -m "quiltimport: $patch_name" HEAD $commit || exit 4
 	fi
 done
 rm -rf $tmp_dir || exit 5
diff --git a/git-rebase.sh b/git-rebase.sh
index 8c5da7219e..cb1a9ce12c 100755
--- a/git-rebase.sh
+++ b/git-rebase.sh
@@ -137,7 +137,8 @@ do
 			finish_rb_merge
 			exit
 		fi
-		git am --resolved --3way --resolvemsg="$RESOLVEMSG"
+		git am --resolved --3way --resolvemsg="$RESOLVEMSG" \
+			--reflog-action=rebase
 		exit
 		;;
 	--skip)
@@ -156,7 +157,8 @@ do
 			finish_rb_merge
 			exit
 		fi
-		git am -3 --skip --resolvemsg="$RESOLVEMSG"
+		git am -3 --skip --resolvemsg="$RESOLVEMSG" \
+			--reflog-action=rebase
 		exit
 		;;
 	--abort)
@@ -299,7 +301,8 @@ fi
 if test -z "$do_merge"
 then
 	git-format-patch -k --stdout --full-index "$upstream"..ORIG_HEAD |
-	git am --binary -3 -k --resolvemsg="$RESOLVEMSG"
+	git am --binary -3 -k --resolvemsg="$RESOLVEMSG" \
+		--reflog-action=rebase
 	exit $?
 fi
 
diff --git a/git-reset.sh b/git-reset.sh
index 5c0224090a..36fc8ce25b 100755
--- a/git-reset.sh
+++ b/git-reset.sh
@@ -52,7 +52,8 @@ then
 else
 	rm -f "$GIT_DIR/ORIG_HEAD"
 fi
-git-update-ref -m "reset $reset_type $@" HEAD "$rev"
+git-update-ref -m "reset $reset_type $*" HEAD "$rev"
+update_ref_status=$?
 
 case "$reset_type" in
 --hard )
@@ -66,3 +67,5 @@ case "$reset_type" in
 esac
 
 rm -f "$GIT_DIR/MERGE_HEAD" "$GIT_DIR/rr-cache/MERGE_RR" "$GIT_DIR/SQUASH_MSG"
+
+exit $update_ref_status
diff --git a/git-resolve.sh b/git-resolve.sh
index 1c7aaefa25..a7bc680d90 100755
--- a/git-resolve.sh
+++ b/git-resolve.sh
@@ -15,6 +15,7 @@ dropheads() {
 
 head=$(git-rev-parse --verify "$1"^0) &&
 merge=$(git-rev-parse --verify "$2"^0) &&
+merge_name="$2" &&
 merge_msg="$3" || usage
 
 #
@@ -43,7 +44,8 @@ case "$common" in
 "$head")
 	echo "Updating from $head to $merge"
 	git-read-tree -u -m $head $merge || exit 1
-	git-update-ref HEAD "$merge" "$head"
+	git-update-ref -m "resolve $merge_name: Fast forward" \
+		HEAD "$merge" "$head"
 	git-diff-tree -p $head $merge | git-apply --stat
 	dropheads
 	exit 0
@@ -100,6 +102,7 @@ if [ $? -ne 0 ]; then
 fi
 result_commit=$(echo "$merge_msg" | git-commit-tree $result_tree -p $head -p $merge)
 echo "Committed merge $result_commit"
-git-update-ref HEAD "$result_commit" "$head"
+git-update-ref -m "resolve $merge_name: In-index merge" \
+	HEAD "$result_commit" "$head"
 git-diff-tree -p $head $result_commit | git-apply --stat
 dropheads
diff --git a/git-svn.perl b/git-svn.perl
index 4530ffe42c..6453771f9c 100755
--- a/git-svn.perl
+++ b/git-svn.perl
@@ -147,7 +147,7 @@ init_vars();
 load_authors() if $_authors;
 load_all_refs() if $_branch_all_refs;
 svn_compat_check() unless $_use_lib;
-migration_check() unless $cmd =~ /^(?:init|rebuild|multi-init)$/;
+migration_check() unless $cmd =~ /^(?:init|rebuild|multi-init|commit-diff)$/;
 $cmd{$cmd}->[0]->(@ARGV);
 exit 0;
 
@@ -2709,6 +2709,12 @@ sub libsvn_fetch {
 			} else {
 				die "Unrecognized action: $m, ($f r$rev)\n";
 			}
+		} elsif ($t == $SVN::Node::dir && $m =~ /^[AR]$/) {
+			my @traversed = ();
+			libsvn_traverse($gui, '', $f, $rev, \@traversed);
+			foreach (@traversed) {
+				push @amr, [ $m, $_ ]
+			}
 		}
 		$pool->clear;
 	}
@@ -2778,7 +2784,7 @@ sub libsvn_parse_revision {
 }
 
 sub libsvn_traverse {
-	my ($gui, $pfx, $path, $rev) = @_;
+	my ($gui, $pfx, $path, $rev, $files) = @_;
 	my $cwd = "$pfx/$path";
 	my $pool = SVN::Pool->new;
 	$cwd =~ s#^/+##g;
@@ -2786,10 +2792,15 @@ sub libsvn_traverse {
 	foreach my $d (keys %$dirent) {
 		my $t = $dirent->{$d}->kind;
 		if ($t == $SVN::Node::dir) {
-			libsvn_traverse($gui, $cwd, $d, $rev);
+			libsvn_traverse($gui, $cwd, $d, $rev, $files);
 		} elsif ($t == $SVN::Node::file) {
-			print "\tA\t$cwd/$d\n" unless $_q;
-			libsvn_get_file($gui, "$cwd/$d", $rev);
+			my $file = "$cwd/$d";
+			if (defined $files) {
+				push @$files, $file;
+			} else {
+				print "\tA\t$file\n" unless $_q;
+				libsvn_get_file($gui, $file, $rev);
+			}
 		}
 	}
 	$pool->clear;
@@ -2913,9 +2924,7 @@ sub libsvn_new_tree {
 	}
 	my ($paths, $rev, $author, $date, $msg) = @_;
 	open my $gui, '| git-update-index -z --index-info' or croak $!;
-	my $pool = SVN::Pool->new;
-	libsvn_traverse($gui, '', $SVN_PATH, $rev, $pool);
-	$pool->clear;
+	libsvn_traverse($gui, '', $SVN_PATH, $rev);
 	close $gui or croak $?;
 	return libsvn_log_entry($rev, $author, $date, $msg);
 }
diff --git a/git.c b/git.c
index 102735af6c..7321d6c3f6 100644
--- a/git.c
+++ b/git.c
@@ -35,6 +35,59 @@ static void prepend_to_path(const char *dir, int len)
 	setenv("PATH", path, 1);
 }
 
+static int handle_options(const char*** argv, int* argc)
+{
+	int handled = 0;
+
+	while (*argc > 0) {
+		const char *cmd = (*argv)[0];
+		if (cmd[0] != '-')
+			break;
+
+		/*
+		 * For legacy reasons, the "version" and "help"
+		 * commands can be written with "--" prepended
+		 * to make them look like flags.
+		 */
+		if (!strcmp(cmd, "--help") || !strcmp(cmd, "--version"))
+			break;
+
+		/*
+		 * Check remaining flags.
+		 */
+		if (!strncmp(cmd, "--exec-path", 11)) {
+			cmd += 11;
+			if (*cmd == '=')
+				git_set_exec_path(cmd + 1);
+			else {
+				puts(git_exec_path());
+				exit(0);
+			}
+		} else if (!strcmp(cmd, "-p") || !strcmp(cmd, "--paginate")) {
+			setup_pager();
+		} else if (!strcmp(cmd, "--git-dir")) {
+			if (*argc < 1)
+				return -1;
+			setenv("GIT_DIR", (*argv)[1], 1);
+			(*argv)++;
+			(*argc)--;
+		} else if (!strncmp(cmd, "--git-dir=", 10)) {
+			setenv("GIT_DIR", cmd + 10, 1);
+		} else if (!strcmp(cmd, "--bare")) {
+			static char git_dir[1024];
+			setenv("GIT_DIR", getcwd(git_dir, 1024), 1);
+		} else {
+			fprintf(stderr, "Unknown option: %s\n", cmd);
+			cmd_usage(0, NULL, NULL);
+		}
+
+		(*argv)++;
+		(*argc)--;
+		handled++;
+	}
+	return handled;
+}
+
 static const char *alias_command;
 static char *alias_string = NULL;
 
@@ -103,49 +156,48 @@ static int handle_alias(int *argcp, const char ***argv)
 {
 	int nongit = 0, ret = 0, saved_errno = errno;
 	const char *subdir;
+	int count, option_count;
+	const char** new_argv;
 
 	subdir = setup_git_directory_gently(&nongit);
-	if (!nongit) {
-		int count;
-		const char** new_argv;
-
-		alias_command = (*argv)[0];
-		git_config(git_alias_config);
-		if (alias_string) {
 
-			count = split_cmdline(alias_string, &new_argv);
+	alias_command = (*argv)[0];
+	git_config(git_alias_config);
+	if (alias_string) {
+		count = split_cmdline(alias_string, &new_argv);
+		option_count = handle_options(&new_argv, &count);
+		memmove(new_argv - option_count, new_argv,
+				count * sizeof(char *));
+		new_argv -= option_count;
 
-			if (count < 1)
-				die("empty alias for %s", alias_command);
+		if (count < 1)
+			die("empty alias for %s", alias_command);
 
-			if (!strcmp(alias_command, new_argv[0]))
-				die("recursive alias: %s", alias_command);
+		if (!strcmp(alias_command, new_argv[0]))
+			die("recursive alias: %s", alias_command);
 
-			if (getenv("GIT_TRACE")) {
-				int i;
-				fprintf(stderr, "trace: alias expansion: %s =>",
-					alias_command);
-				for (i = 0; i < count; ++i) {
-					fputc(' ', stderr);
-					sq_quote_print(stderr, new_argv[i]);
-				}
-				fputc('\n', stderr);
-				fflush(stderr);
+		if (getenv("GIT_TRACE")) {
+			int i;
+			fprintf(stderr, "trace: alias expansion: %s =>",
+				alias_command);
+			for (i = 0; i < count; ++i) {
+				fputc(' ', stderr);
+				sq_quote_print(stderr, new_argv[i]);
 			}
+			fputc('\n', stderr);
+			fflush(stderr);
+		}
 
-			/* insert after command name */
-			if (*argcp > 1) {
-				new_argv = realloc(new_argv, sizeof(char*) *
-						   (count + *argcp));
-				memcpy(new_argv + count, *argv + 1,
-				       sizeof(char*) * *argcp);
-			}
+		new_argv = realloc(new_argv, sizeof(char*) *
+				   (count + *argcp + 1));
+		/* insert after command name */
+		memcpy(new_argv + count, *argv + 1, sizeof(char*) * *argcp);
+		new_argv[count+*argcp] = NULL;
 
-			*argv = new_argv;
-			*argcp += count - 1;
+		*argv = new_argv;
+		*argcp += count - 1;
 
-			ret = 1;
-		}
+		ret = 1;
 	}
 
 	if (subdir)
@@ -158,51 +210,55 @@ static int handle_alias(int *argcp, const char ***argv)
 
 const char git_version_string[] = GIT_VERSION;
 
+#define NEEDS_PREFIX 1
+
 static void handle_internal_command(int argc, const char **argv, char **envp)
 {
 	const char *cmd = argv[0];
 	static struct cmd_struct {
 		const char *cmd;
-		int (*fn)(int, const char **, char **);
+		int (*fn)(int, const char **, const char *);
+		int prefix;
 	} commands[] = {
 		{ "version", cmd_version },
 		{ "help", cmd_help },
-		{ "log", cmd_log },
-		{ "whatchanged", cmd_whatchanged },
-		{ "show", cmd_show },
+		{ "log", cmd_log, NEEDS_PREFIX },
+		{ "whatchanged", cmd_whatchanged, NEEDS_PREFIX },
+		{ "show", cmd_show, NEEDS_PREFIX },
 		{ "push", cmd_push },
-		{ "format-patch", cmd_format_patch },
+		{ "format-patch", cmd_format_patch, NEEDS_PREFIX },
 		{ "count-objects", cmd_count_objects },
-		{ "diff", cmd_diff },
-		{ "grep", cmd_grep },
-		{ "rm", cmd_rm },
-		{ "add", cmd_add },
-		{ "rev-list", cmd_rev_list },
+		{ "diff", cmd_diff, NEEDS_PREFIX },
+		{ "grep", cmd_grep, NEEDS_PREFIX },
+		{ "rm", cmd_rm, NEEDS_PREFIX },
+		{ "add", cmd_add, NEEDS_PREFIX },
+		{ "rev-list", cmd_rev_list, NEEDS_PREFIX },
 		{ "init-db", cmd_init_db },
 		{ "get-tar-commit-id", cmd_get_tar_commit_id },
 		{ "upload-tar", cmd_upload_tar },
 		{ "check-ref-format", cmd_check_ref_format },
-		{ "ls-files", cmd_ls_files },
-		{ "ls-tree", cmd_ls_tree },
-		{ "tar-tree", cmd_tar_tree },
-		{ "read-tree", cmd_read_tree },
-		{ "commit-tree", cmd_commit_tree },
+		{ "ls-files", cmd_ls_files, NEEDS_PREFIX },
+		{ "ls-tree", cmd_ls_tree, NEEDS_PREFIX },
+		{ "tar-tree", cmd_tar_tree, NEEDS_PREFIX },
+		{ "read-tree", cmd_read_tree, NEEDS_PREFIX },
+		{ "commit-tree", cmd_commit_tree, NEEDS_PREFIX },
 		{ "apply", cmd_apply },
-		{ "show-branch", cmd_show_branch },
-		{ "diff-files", cmd_diff_files },
-		{ "diff-index", cmd_diff_index },
-		{ "diff-stages", cmd_diff_stages },
-		{ "diff-tree", cmd_diff_tree },
-		{ "cat-file", cmd_cat_file },
-		{ "rev-parse", cmd_rev_parse },
-		{ "write-tree", cmd_write_tree },
+		{ "show-branch", cmd_show_branch, NEEDS_PREFIX },
+		{ "diff-files", cmd_diff_files, NEEDS_PREFIX },
+		{ "diff-index", cmd_diff_index, NEEDS_PREFIX },
+		{ "diff-stages", cmd_diff_stages, NEEDS_PREFIX },
+		{ "diff-tree", cmd_diff_tree, NEEDS_PREFIX },
+		{ "cat-file", cmd_cat_file, NEEDS_PREFIX },
+		{ "rev-parse", cmd_rev_parse, NEEDS_PREFIX },
+		{ "write-tree", cmd_write_tree, NEEDS_PREFIX },
 		{ "mailsplit", cmd_mailsplit },
 		{ "mailinfo", cmd_mailinfo },
 		{ "stripspace", cmd_stripspace },
-		{ "update-index", cmd_update_index },
-		{ "update-ref", cmd_update_ref },
-		{ "fmt-merge-msg", cmd_fmt_merge_msg },
-		{ "prune", cmd_prune },
+		{ "update-index", cmd_update_index, NEEDS_PREFIX },
+		{ "update-ref", cmd_update_ref, NEEDS_PREFIX },
+		{ "fmt-merge-msg", cmd_fmt_merge_msg, NEEDS_PREFIX },
+		{ "prune", cmd_prune, NEEDS_PREFIX },
+		{ "mv", cmd_mv, NEEDS_PREFIX },
 	};
 	int i;
 
@@ -214,9 +270,13 @@ static void handle_internal_command(int argc, const char **argv, char **envp)
 
 	for (i = 0; i < ARRAY_SIZE(commands); i++) {
 		struct cmd_struct *p = commands+i;
+		const char *prefix;
 		if (strcmp(p->cmd, cmd))
 			continue;
 
+		prefix = NULL;
+		if (p->prefix)
+			prefix = setup_git_directory();
 		if (getenv("GIT_TRACE")) {
 			int i;
 			fprintf(stderr, "trace: built-in: git");
@@ -228,7 +288,7 @@ static void handle_internal_command(int argc, const char **argv, char **envp)
 			fflush(stderr);
 		}
 
-		exit(p->fn(argc, argv, envp));
+		exit(p->fn(argc, argv, prefix));
 	}
 }
 
@@ -269,51 +329,19 @@ int main(int argc, const char **argv, char **envp)
 		die("cannot handle %s internally", cmd);
 	}
 
-	/* Default command: "help" */
-	cmd = "help";
-
 	/* Look for flags.. */
-	while (argc > 1) {
-		cmd = *++argv;
-		argc--;
-
-		if (!strcmp(cmd, "-p") || !strcmp(cmd, "--paginate")) {
-			setup_pager();
-			continue;
-		}
-
-		if (strncmp(cmd, "--", 2))
-			break;
-
-		cmd += 2;
-
-		/*
-		 * For legacy reasons, the "version" and "help"
-		 * commands can be written with "--" prepended
-		 * to make them look like flags.
-		 */
-		if (!strcmp(cmd, "help"))
-			break;
-		if (!strcmp(cmd, "version"))
-			break;
-
-		/*
-		 * Check remaining flags (which by now must be
-		 * "--exec-path", but maybe we will accept
-		 * other arguments some day)
-		 */
-		if (!strncmp(cmd, "exec-path", 9)) {
-			cmd += 9;
-			if (*cmd == '=') {
-				git_set_exec_path(cmd + 1);
-				continue;
-			}
-			puts(git_exec_path());
-			exit(0);
-		}
-		cmd_usage(0, NULL, NULL);
+	argv++;
+	argc--;
+	handle_options(&argv, &argc);
+	if (argc > 0) {
+		if (!strncmp(argv[0], "--", 2))
+			argv[0] += 2;
+	} else {
+		/* Default command: "help" */
+		argv[0] = "help";
+		argc = 1;
 	}
-	argv[0] = cmd;
+	cmd = argv[0];
 
 	/*
 	 * We search for git commands in the following order:
diff --git a/gitweb/gitweb.cgi b/gitweb/gitweb.cgi
index 2fd1e5f78e..e5fca63b9c 100755
--- a/gitweb/gitweb.cgi
+++ b/gitweb/gitweb.cgi
@@ -227,7 +227,7 @@ if (!defined $action || $action eq "summary") {
 	git_tag();
 	exit;
 } elsif ($action eq "blame") {
-	git_blame();
+	git_blame2();
 	exit;
 } else {
 	undef $action;
@@ -795,7 +795,7 @@ sub git_read_projects {
 	if (-d $projects_list) {
 		# search in directory
 		my $dir = $projects_list;
-		opendir my $dh, $dir or return undef;
+		opendir my ($dh), $dir or return undef;
 		while (my $dir = readdir($dh)) {
 			if (-e "$projectroot/$dir/HEAD") {
 				my $pr = {
@@ -810,7 +810,7 @@ sub git_read_projects {
 		# 'git%2Fgit.git Linus+Torvalds'
 		# 'libs%2Fklibc%2Fklibc.git H.+Peter+Anvin'
 		# 'linux%2Fhotplug%2Fudev.git Greg+Kroah-Hartman'
-		open my $fd , $projects_list or return undef;
+		open my ($fd), $projects_list or return undef;
 		while (my $line = <$fd>) {
 			chomp $line;
 			my ($path, $owner) = split ' ', $line;
@@ -1138,7 +1138,7 @@ sub git_summary {
 				      "</td>\n" .
 				      "<td>";
 				if (defined($comment)) {
-				      print $cgi->a({-class => "list", -href => "$my_uri?" . esc_param("p=$project;a=tag;h=$tag{'id'}")}, $comment);
+				      print $cgi->a({-class => "list", -href => "$my_uri?" . esc_param("p=$project;a=tag;h=$tag{'id'}")}, esc_html($comment));
 				}
 				print "</td>\n" .
 				      "<td class=\"link\">";
@@ -1199,6 +1199,20 @@ sub git_summary {
 	git_footer_html();
 }
 
+sub git_print_page_path {
+	my $name = shift;
+	my $type = shift;
+
+	if (!defined $name) {
+		print "<div class=\"page_path\"><b>/</b></div>\n";
+	} elsif ($type =~ "blob") {
+		print "<div class=\"page_path\"><b>" .
+			$cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blob_plain;f=$file_name")}, esc_html($name)) . "</b><br/></div>\n";
+	} else {
+		print "<div class=\"page_path\"><b>" . esc_html($name) . "</b><br/></div>\n";
+	}
+}
+
 sub git_tag {
 	my $head = git_read_head($project);
 	git_header_html();
@@ -1238,6 +1252,73 @@ sub git_tag {
 	git_footer_html();
 }
 
+sub git_blame2 {
+	my $fd;
+	my $ftype;
+	die_error(undef, "Permission denied.") if (!git_get_project_config_bool ('blame'));
+	die_error('404 Not Found', "File name not defined") if (!$file_name);
+	$hash_base ||= git_read_head($project);
+	die_error(undef, "Reading commit failed") unless ($hash_base);
+	my %co = git_read_commit($hash_base)
+		or die_error(undef, "Reading commit failed");
+	if (!defined $hash) {
+		$hash = git_get_hash_by_path($hash_base, $file_name, "blob")
+			or die_error(undef, "Error looking up file");
+	}
+	$ftype = git_get_type($hash);
+	if ($ftype !~ "blob") {
+		die_error("400 Bad Request", "object is not a blob");
+	}
+	open ($fd, "-|", $GIT, "blame", '-l', $file_name, $hash_base)
+		or die_error(undef, "Open failed");
+	git_header_html();
+	print "<div class=\"page_nav\">\n" .
+		$cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=summary")}, "summary") .
+		" | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=shortlog")}, "shortlog") .
+		" | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=log")}, "log") .
+		" | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$hash_base")}, "commit") .
+		" | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commitdiff;h=$hash_base")}, "commitdiff") .
+		" | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=tree;h=$co{'tree'};hb=$hash_base")}, "tree") . "<br/>\n";
+	print $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blob;h=$hash;hb=$hash_base;f=$file_name")}, "blob") .
+		" | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blame;f=$file_name")}, "head") . "<br/>\n";
+	print "</div>\n".
+		"<div>" .
+		$cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$hash_base"), -class => "title"}, esc_html($co{'title'})) .
+		"</div>\n";
+	git_print_page_path($file_name, $ftype);
+	my @rev_color = (qw(light dark));
+	my $num_colors = scalar(@rev_color);
+	my $current_color = 0;
+	my $last_rev;
+	print "<div class=\"page_body\">\n";
+	print "<table class=\"blame\">\n";
+	print "<tr><th>Commit</th><th>Line</th><th>Data</th></tr>\n";
+	while (<$fd>) {
+		/^([0-9a-fA-F]{40}).*?(\d+)\)\s{1}(\s*.*)/;
+		my $full_rev = $1;
+		my $rev = substr($full_rev, 0, 8);
+		my $lineno = $2;
+		my $data = $3;
+
+		if (!defined $last_rev) {
+			$last_rev = $full_rev;
+		} elsif ($last_rev ne $full_rev) {
+			$last_rev = $full_rev;
+			$current_color = ++$current_color % $num_colors;
+		}
+		print "<tr class=\"$rev_color[$current_color]\">\n";
+		print "<td class=\"sha1\">" .
+			$cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$full_rev;f=$file_name")}, esc_html($rev)) . "</td>\n";
+		print "<td class=\"linenr\"><a id=\"l$lineno\" href=\"#l$lineno\" class=\"linenr\">" . esc_html($lineno) . "</a></td>\n";
+		print "<td class=\"pre\">" . esc_html($data) . "</td>\n";
+		print "</tr>\n";
+	}
+	print "</table>\n";
+	print "</div>";
+	close $fd or print "Reading blob failed\n";
+	git_footer_html();
+}
+
 sub git_blame {
 	my $fd;
 	die_error('403 Permission denied', "Permission denied.") if (!git_get_project_config_bool ('blame'));
@@ -1266,7 +1347,7 @@ sub git_blame {
 		"<div>" .
 		$cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$hash_base"), -class => "title"}, esc_html($co{'title'})) .
 		"</div>\n";
-	print "<div class=\"page_path\"><b>" . esc_html($file_name) . "</b></div>\n";
+	git_print_page_path($file_name);
 	print "<div class=\"page_body\">\n";
 	print <<HTML;
 <table class="blame">
@@ -1531,6 +1612,14 @@ sub git_blob_plain_mimetype {
 }
 
 sub git_blob_plain {
+	if (!defined $hash) {
+                if (defined $file_name) {
+                        my $base = $hash_base || git_read_head($project);
+                        $hash = git_get_hash_by_path($base, $file_name, "blob") || die_error(undef, "Error lookup file.");
+                } else {
+                        die_error(undef, "No file name defined.");
+                }
+        }
 	my $type = shift;
 	open my $fd, "-|", "$GIT cat-file blob $hash" or die_error("Couldn't cat $file_name, $hash");
 
@@ -1554,10 +1643,14 @@ sub git_blob_plain {
 }
 
 sub git_blob {
-	if (!defined $hash && defined $file_name) {
-		my $base = $hash_base || git_read_head($project);
-		$hash = git_get_hash_by_path($base, $file_name, "blob") || die_error(undef, "Error lookup file.");
-	}
+	if (!defined $hash) {
+                if (defined $file_name) {
+                        my $base = $hash_base || git_read_head($project);
+                        $hash = git_get_hash_by_path($base, $file_name, "blob") || die_error(undef, "Error lookup file.");
+                } else {
+                        die_error(undef, "No file name defined.");
+                }
+        }
 	my $have_blame = git_get_project_config_bool ('blame');
 	open my $fd, "-|", "$GIT cat-file blob $hash" or die_error(undef, "Open failed.");
 	my $mimetype = git_blob_plain_mimetype($fd, $file_name);
@@ -1592,9 +1685,7 @@ sub git_blob {
 		      "<br/><br/></div>\n" .
 		      "<div class=\"title\">$hash</div>\n";
 	}
-	if (defined $file_name) {
-		print "<div class=\"page_path\"><b>" . esc_html($file_name) . "</b></div>\n";
-	}
+	git_print_page_path($file_name, "blob");
 	print "<div class=\"page_body\">\n";
 	my $nr;
 	while (my $line = <$fd>) {
@@ -1659,10 +1750,8 @@ sub git_tree {
 	}
 	if (defined $file_name) {
 		$base = esc_html("$file_name/");
-		print "<div class=\"page_path\"><b>/" . esc_html($file_name) . "</b></div>\n";
-	} else {
-		print "<div class=\"page_path\"><b>/</b></div>\n";
 	}
+	git_print_page_path($file_name);
 	print "<div class=\"page_body\">\n";
 	print "<table cellspacing=\"0\">\n";
 	my $alternate = 0;
@@ -1687,7 +1776,7 @@ sub git_tree {
 			      "<td class=\"link\">" .
 			      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blob;h=$t_hash$base_key;f=$base$t_name")}, "blob") .
 #			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blame;h=$t_hash$base_key;f=$base$t_name")}, "blame") .
-			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;h=$hash_base;f=$base$t_name")}, "history") .
+			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;h=$t_hash;hb=$hash_base;f=$base$t_name")}, "history") .
 			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blob_plain;h=$t_hash;f=$base$t_name")}, "raw") .
 			      "</td>\n";
 		} elsif ($t_type eq "tree") {
@@ -1696,7 +1785,7 @@ sub git_tree {
 			      "</td>\n" .
 			      "<td class=\"link\">" .
 			      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=tree;h=$t_hash$base_key;f=$base$t_name")}, "tree") .
-			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;h=$hash_base;f=$base$t_name")}, "history") .
+			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;hb=$hash_base;f=$base$t_name")}, "history") .
 			      "</td>\n";
 		}
 		print "</tr>\n";
@@ -1931,7 +2020,13 @@ sub git_commit {
 		print " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commitdiff;h=$hash")}, "commitdiff");
 	}
 	print " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=tree;h=$co{'tree'};hb=$hash")}, "tree") . "\n" .
-	      "<br/><br/></div>\n";
+		"<br/>\n";
+	if (defined $file_name && defined $co{'parent'}) {
+		my $parent = $co{'parent'};
+		print $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blame;hb=$parent;f=$file_name")}, "blame") . "\n";
+	}
+	print "<br/></div>\n";
+
 	if (defined $co{'parent'}) {
 		print "<div>\n" .
 		      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commitdiff;h=$hash"), -class => "title"}, esc_html($co{'title'}) . $ref) . "\n" .
@@ -2041,7 +2136,7 @@ sub git_commit {
 			      "<td><span class=\"file_status deleted\">[deleted " . file_type($from_mode). "]</span></td>\n" .
 			      "<td class=\"link\">" .
 			      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blob;h=$from_id;hb=$hash;f=$file")}, "blob") .
-			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;h=$hash;f=$file")}, "history") .
+			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;hb=$hash;f=$file")}, "history") .
 			      "</td>\n"
 		} elsif ($status eq "M" || $status eq "T") {
 			my $mode_chnge = "";
@@ -2072,7 +2167,7 @@ sub git_commit {
 			if ($to_id ne $from_id) {
 				print " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blobdiff;h=$to_id;hp=$from_id;hb=$hash;f=$file")}, "diff");
 			}
-			print " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;h=$hash;f=$file")}, "history") . "\n";
+			print " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=history;hb=$hash;f=$file")}, "history") . "\n";
 			print "</td>\n";
 		} elsif ($status eq "R") {
 			my ($from_file, $to_file) = split "\t", $file;
@@ -2120,9 +2215,7 @@ sub git_blobdiff {
 		      "<br/><br/></div>\n" .
 		      "<div class=\"title\">$hash vs $hash_parent</div>\n";
 	}
-	if (defined $file_name) {
-		print "<div class=\"page_path\"><b>/" . esc_html($file_name) . "</b></div>\n";
-	}
+	git_print_page_path($file_name, "blob");
 	print "<div class=\"page_body\">\n" .
 	      "<div class=\"diff_info\">blob:" .
 	      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blob;h=$hash_parent;hb=$hash_base;f=$file_name")}, $hash_parent) .
@@ -2293,10 +2386,11 @@ sub git_commitdiff_plain {
 }
 
 sub git_history {
-	if (!defined $hash) {
-		$hash = git_read_head($project);
+	if (!defined $hash_base) {
+		$hash_base = git_read_head($project);
 	}
-	my %co = git_read_commit($hash);
+	my $ftype;
+	my %co = git_read_commit($hash_base);
 	if (!%co) {
 		die_error(undef, "Unknown commit object.");
 	}
@@ -2306,18 +2400,24 @@ sub git_history {
 	      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=summary")}, "summary") .
 	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=shortlog")}, "shortlog") .
 	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=log")}, "log") .
-	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$hash")}, "commit") .
-	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commitdiff;h=$hash")}, "commitdiff") .
-	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=tree;h=$co{'tree'};hb=$hash")}, "tree") .
+	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$hash_base")}, "commit") .
+	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commitdiff;h=$hash_base")}, "commitdiff") .
+	      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=tree;h=$co{'tree'};hb=$hash_base")}, "tree") .
 	      "<br/><br/>\n" .
 	      "</div>\n";
 	print "<div>\n" .
-	      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$hash"), -class => "title"}, esc_html($co{'title'})) . "\n" .
+	      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$hash_base"), -class => "title"}, esc_html($co{'title'})) . "\n" .
 	      "</div>\n";
-	print "<div class=\"page_path\"><b>/" . esc_html($file_name) . "</b><br/></div>\n";
+	if (!defined $hash && defined $file_name) {
+		$hash = git_get_hash_by_path($hash_base, $file_name);
+	}
+	if (defined $hash) {
+		$ftype = git_get_type($hash);
+	}
+	git_print_page_path($file_name, $ftype);
 
 	open my $fd, "-|",
-		"$GIT rev-list --full-history $hash -- \'$file_name\'";
+		"$GIT rev-list --full-history $hash_base -- \'$file_name\'";
 	print "<table cellspacing=\"0\">\n";
 	my $alternate = 0;
 	while (my $line = <$fd>) {
@@ -2345,7 +2445,7 @@ sub git_history {
 			      $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commit;h=$commit")}, "commit") .
 			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=commitdiff;h=$commit")}, "commitdiff") .
 			      " | " . $cgi->a({-href => "$my_uri?" . esc_param("p=$project;a=blob;hb=$commit;f=$file_name")}, "blob");
-			my $blob = git_get_hash_by_path($hash, $file_name);
+			my $blob = git_get_hash_by_path($hash_base, $file_name);
 			my $blob_parent = git_get_hash_by_path($commit, $file_name);
 			if (defined $blob && defined $blob_parent && $blob ne $blob_parent) {
 				print " | " .
diff --git a/http-fetch.c b/http-fetch.c
index 12493fbed2..1aad39b4d8 100644
--- a/http-fetch.c
+++ b/http-fetch.c
@@ -36,6 +36,8 @@ enum XML_Status {
 #define PREV_BUF_SIZE 4096
 #define RANGE_HEADER_SIZE 30
 
+static int commits_on_stdin = 0;
+
 static int got_alternates = -1;
 static int corrupt_object_found = 0;
 
@@ -43,7 +45,7 @@ static struct curl_slist *no_pragma_header;
 
 struct alt_base
 {
-	char *base;
+	const char *base;
 	int path_len;
 	int got_indices;
 	struct packed_git *packs;
@@ -81,7 +83,7 @@ struct object_request
 };
 
 struct alternates_request {
-	char *base;
+	const char *base;
 	char *url;
 	struct buffer *buffer;
 	struct active_request_slot *slot;
@@ -142,7 +144,7 @@ static size_t fwrite_sha1_file(void *ptr, size_t eltsize, size_t nmemb,
 	return size;
 }
 
-static void fetch_alternates(char *base);
+static void fetch_alternates(const char *base);
 
 static void process_object_response(void *callback_data);
 
@@ -507,7 +509,7 @@ static void process_alternates_response(void *callback_data)
 		(struct alternates_request *)callback_data;
 	struct active_request_slot *slot = alt_req->slot;
 	struct alt_base *tail = alt;
-	char *base = alt_req->base;
+	const char *base = alt_req->base;
 	static const char null_byte = '\0';
 	char *data;
 	int i = 0;
@@ -612,7 +614,7 @@ static void process_alternates_response(void *callback_data)
 	got_alternates = 1;
 }
 
-static void fetch_alternates(char *base)
+static void fetch_alternates(const char *base)
 {
 	struct buffer buffer;
 	char *url;
@@ -1185,7 +1187,7 @@ int fetch_ref(char *ref, unsigned char *sha1)
         char *url;
         char hex[42];
         struct buffer buffer;
-	char *base = alt->base;
+	const char *base = alt->base;
 	struct active_request_slot *slot;
 	struct slot_results results;
         buffer.size = 41;
@@ -1214,10 +1216,12 @@ int fetch_ref(char *ref, unsigned char *sha1)
         return 0;
 }
 
-int main(int argc, char **argv)
+int main(int argc, const char **argv)
 {
-	char *commit_id;
-	char *url;
+	int commits;
+	const char **write_ref = NULL;
+	char **commit_id;
+	const char *url;
 	char *path;
 	int arg = 1;
 	int rc = 0;
@@ -1237,20 +1241,26 @@ int main(int argc, char **argv)
 		} else if (argv[arg][1] == 'v') {
 			get_verbosely = 1;
 		} else if (argv[arg][1] == 'w') {
-			write_ref = argv[arg + 1];
+			write_ref = &argv[arg + 1];
 			arg++;
 		} else if (!strcmp(argv[arg], "--recover")) {
 			get_recover = 1;
+		} else if (!strcmp(argv[arg], "--stdin")) {
+			commits_on_stdin = 1;
 		}
 		arg++;
 	}
-	if (argc < arg + 2) {
-		usage("git-http-fetch [-c] [-t] [-a] [-d] [-v] [--recover] [-w ref] commit-id url");
+	if (argc < arg + 2 - commits_on_stdin) {
+		usage("git-http-fetch [-c] [-t] [-a] [-v] [--recover] [-w ref] [--stdin] commit-id url");
 		return 1;
 	}
-	commit_id = argv[arg];
-	url = argv[arg + 1];
-	write_ref_log_details = url;
+	if (commits_on_stdin) {
+		commits = pull_targets_stdin(&commit_id, &write_ref);
+	} else {
+		commit_id = (char **) &argv[arg++];
+		commits = 1;
+	}
+	url = argv[arg];
 
 	http_init();
 
@@ -1268,13 +1278,16 @@ int main(int argc, char **argv)
 			alt->path_len = strlen(path);
 	}
 
-	if (pull(commit_id))
+	if (pull(commits, commit_id, write_ref, url))
 		rc = 1;
 
 	http_cleanup();
 
 	curl_slist_free_all(no_pragma_header);
 
+	if (commits_on_stdin)
+		pull_targets_free(commits, commit_id, write_ref);
+
 	if (corrupt_object_found) {
 		fprintf(stderr,
 "Some loose object were found to be corrupt, but they might be just\n"
diff --git a/http-push.c b/http-push.c
index 47686195cd..4021e7d927 100644
--- a/http-push.c
+++ b/http-push.c
@@ -2521,7 +2521,7 @@ int main(int argc, char **argv)
 			commit_argv[3] = old_sha1_hex;
 			commit_argc++;
 		}
-		init_revisions(&revs);
+		init_revisions(&revs, setup_git_directory());
 		setup_revisions(commit_argc, commit_argv, &revs, NULL);
 		free(new_sha1_hex);
 		if (old_sha1_hex) {
diff --git a/local-fetch.c b/local-fetch.c
index ffa4887570..b216bdd557 100644
--- a/local-fetch.c
+++ b/local-fetch.c
@@ -8,8 +8,9 @@
 static int use_link = 0;
 static int use_symlink = 0;
 static int use_filecopy = 1;
+static int commits_on_stdin = 0;
 
-static char *path; /* "Remote" git repository */
+static const char *path; /* "Remote" git repository */
 
 void prefetch(unsigned char *sha1)
 {
@@ -194,17 +195,19 @@ int fetch_ref(char *ref, unsigned char *sha1)
 }
 
 static const char local_pull_usage[] =
-"git-local-fetch [-c] [-t] [-a] [-d] [-v] [-w filename] [--recover] [-l] [-s] [-n] commit-id path";
+"git-local-fetch [-c] [-t] [-a] [-v] [-w filename] [--recover] [-l] [-s] [-n] [--stdin] commit-id path";
 
-/* 
+/*
  * By default we only use file copy.
  * If -l is specified, a hard link is attempted.
  * If -s is specified, then a symlink is attempted.
  * If -n is _not_ specified, then a regular file-to-file copy is done.
  */
-int main(int argc, char **argv)
+int main(int argc, const char **argv)
 {
-	char *commit_id;
+	int commits;
+	const char **write_ref = NULL;
+	char **commit_id;
 	int arg = 1;
 
 	setup_git_directory();
@@ -229,21 +232,30 @@ int main(int argc, char **argv)
 		else if (argv[arg][1] == 'v')
 			get_verbosely = 1;
 		else if (argv[arg][1] == 'w')
-			write_ref = argv[++arg];
+			write_ref = &argv[++arg];
 		else if (!strcmp(argv[arg], "--recover"))
 			get_recover = 1;
+		else if (!strcmp(argv[arg], "--stdin"))
+			commits_on_stdin = 1;
 		else
 			usage(local_pull_usage);
 		arg++;
 	}
-	if (argc < arg + 2)
+	if (argc < arg + 2 - commits_on_stdin)
 		usage(local_pull_usage);
-	commit_id = argv[arg];
-	path = argv[arg + 1];
-	write_ref_log_details = path;
+	if (commits_on_stdin) {
+		commits = pull_targets_stdin(&commit_id, &write_ref);
+	} else {
+		commit_id = (char **) &argv[arg++];
+		commits = 1;
+	}
+	path = argv[arg];
 
-	if (pull(commit_id))
+	if (pull(commits, commit_id, write_ref, path))
 		return 1;
 
+	if (commits_on_stdin)
+		pull_targets_free(commits, commit_id, write_ref);
+
 	return 0;
 }
diff --git a/log-tree.c b/log-tree.c
index 9d8d46fa00..b67b8dd17a 100644
--- a/log-tree.c
+++ b/log-tree.c
@@ -97,6 +97,11 @@ void show_log(struct rev_info *opt, const char *sep)
 			subject = "Subject: ";
 
 		printf("From %s Mon Sep 17 00:00:00 2001\n", sha1);
+		if (opt->message_id)
+			printf("Message-Id: <%s>\n", opt->message_id);
+		if (opt->ref_message_id)
+			printf("In-Reply-To: <%s>\nReferences: <%s>\n",
+			       opt->ref_message_id, opt->ref_message_id);
 		if (opt->mime_boundary) {
 			static char subject_buffer[1024];
 			static char buffer[1024];
@@ -129,7 +134,8 @@ void show_log(struct rev_info *opt, const char *sep)
 			opt->diffopt.stat_sep = buffer;
 		}
 	} else {
-		printf("%s%s",
+		printf("%s%s%s",
+		       diff_get_color(opt->diffopt.color_diff, DIFF_COMMIT),
 		       opt->commit_format == CMIT_FMT_ONELINE ? "" : "commit ",
 		       diff_unique_abbrev(commit->object.sha1, abbrev_commit));
 		if (opt->parents)
@@ -138,6 +144,8 @@ void show_log(struct rev_info *opt, const char *sep)
 			printf(" (from %s)",
 			       diff_unique_abbrev(parent->object.sha1,
 						  abbrev_commit));
+		printf("%s",
+		       diff_get_color(opt->diffopt.color_diff, DIFF_RESET));
 		putchar(opt->commit_format == CMIT_FMT_ONELINE ? ' ' : '\n');
 	}
 
diff --git a/pack-objects.c b/pack-objects.c
index 04a48b925b..861c7f08ff 100644
--- a/pack-objects.c
+++ b/pack-objects.c
@@ -63,6 +63,7 @@ static const char *base_name;
 static unsigned char pack_file_sha1[20];
 static int progress = 1;
 static volatile sig_atomic_t progress_update = 0;
+static int window = 10;
 
 /*
  * The object names in objects array are hashed with this hashtable,
@@ -1216,16 +1217,26 @@ static void setup_progress_signal(void)
 	setitimer(ITIMER_REAL, &v, NULL);
 }
 
+static int git_pack_config(const char *k, const char *v)
+{
+	if(!strcmp(k, "pack.window")) {
+		window = git_config_int(k, v);
+		return 0;
+	}
+	return git_default_config(k, v);
+}
+
 int main(int argc, char **argv)
 {
 	SHA_CTX ctx;
 	char line[40 + 1 + PATH_MAX + 2];
-	int window = 10, depth = 10, pack_to_stdout = 0;
+	int depth = 10, pack_to_stdout = 0;
 	struct object_entry **list;
 	int num_preferred_base = 0;
 	int i;
 
 	setup_git_directory();
+	git_config(git_pack_config);
 
 	progress = isatty(2);
 	for (i = 1; i < argc; i++) {
diff --git a/read-cache.c b/read-cache.c
index 9c0a9fc2a1..c375e912a9 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -319,6 +319,45 @@ int remove_file_from_cache(const char *path)
 	return 0;
 }
 
+int add_file_to_index(const char *path, int verbose)
+{
+	int size, namelen;
+	struct stat st;
+	struct cache_entry *ce;
+
+	if (lstat(path, &st))
+		die("%s: unable to stat (%s)", path, strerror(errno));
+
+	if (!S_ISREG(st.st_mode) && !S_ISLNK(st.st_mode))
+		die("%s: can only add regular files or symbolic links", path);
+
+	namelen = strlen(path);
+	size = cache_entry_size(namelen);
+	ce = xcalloc(1, size);
+	memcpy(ce->name, path, namelen);
+	ce->ce_flags = htons(namelen);
+	fill_stat_cache_info(ce, &st);
+
+	ce->ce_mode = create_ce_mode(st.st_mode);
+	if (!trust_executable_bit) {
+		/* If there is an existing entry, pick the mode bits
+		 * from it.
+		 */
+		int pos = cache_name_pos(path, namelen);
+		if (pos >= 0)
+			ce->ce_mode = active_cache[pos]->ce_mode;
+	}
+
+	if (index_path(ce->sha1, path, &st, 1))
+		die("unable to index file %s", path);
+	if (add_cache_entry(ce, ADD_CACHE_OK_TO_ADD))
+		die("unable to add %s to index",path);
+	if (verbose)
+		printf("add '%s'\n", path);
+	cache_tree_invalidate_path(active_cache_tree, path);
+	return 0;
+}
+
 int ce_same_name(struct cache_entry *a, struct cache_entry *b)
 {
 	int len = ce_namelen(a);
diff --git a/refs.c b/refs.c
index 56db394459..02850b6908 100644
--- a/refs.c
+++ b/refs.c
@@ -294,6 +294,7 @@ static struct ref_lock *lock_ref_sha1_basic(const char *path,
 	int plen,
 	const unsigned char *old_sha1, int mustexist)
 {
+	const char *orig_path = path;
 	struct ref_lock *lock;
 	struct stat st;
 
@@ -303,7 +304,11 @@ static struct ref_lock *lock_ref_sha1_basic(const char *path,
 	plen = strlen(path) - plen;
 	path = resolve_ref(path, lock->old_sha1, mustexist);
 	if (!path) {
+		int last_errno = errno;
+		error("unable to resolve reference %s: %s",
+			orig_path, strerror(errno));
 		unlock_ref(lock);
+		errno = last_errno;
 		return NULL;
 	}
 	lock->lk = xcalloc(1, sizeof(struct lock_file));
diff --git a/revision.c b/revision.c
index 874e349db8..a58257ad80 100644
--- a/revision.c
+++ b/revision.c
@@ -509,7 +509,7 @@ static int add_parents_only(struct rev_info *revs, const char *arg, int flags)
 	return 1;
 }
 
-void init_revisions(struct rev_info *revs)
+void init_revisions(struct rev_info *revs, const char *prefix)
 {
 	memset(revs, 0, sizeof(*revs));
 
@@ -521,7 +521,7 @@ void init_revisions(struct rev_info *revs)
 	revs->pruning.change = file_change;
 	revs->lifo = 1;
 	revs->dense = 1;
-	revs->prefix = setup_git_directory();
+	revs->prefix = prefix;
 	revs->max_age = -1;
 	revs->min_age = -1;
 	revs->max_count = -1;
diff --git a/revision.h b/revision.h
index c010a08116..0c3b8d9905 100644
--- a/revision.h
+++ b/revision.h
@@ -61,6 +61,8 @@ struct rev_info {
 	struct log_info *loginfo;
 	int		nr, total;
 	const char	*mime_boundary;
+	const char	*message_id;
+	const char	*ref_message_id;
 	const char	*add_signoff;
 	const char	*extra_headers;
 
@@ -85,7 +87,7 @@ struct rev_info {
 extern int rev_same_tree_as_empty(struct rev_info *, struct tree *t1);
 extern int rev_compare_tree(struct rev_info *, struct tree *t1, struct tree *t2);
 
-extern void init_revisions(struct rev_info *revs);
+extern void init_revisions(struct rev_info *revs, const char *prefix);
 extern int setup_revisions(int argc, const char **argv, struct rev_info *revs, const char *def);
 extern void prepare_revision_walk(struct rev_info *revs);
 extern struct commit *get_revision(struct rev_info *revs);
diff --git a/setup.c b/setup.c
index 4612f110ee..358e139d84 100644
--- a/setup.c
+++ b/setup.c
@@ -184,6 +184,10 @@ const char *setup_git_directory_gently(int *nongit_ok)
 		}
 		return NULL;
 	bad_dir_environ:
+		if (!nongit_ok) {
+			*nongit_ok = 1;
+			return NULL;
+		}
 		path[len] = 0;
 		die("Not a git repository: '%s'", path);
 	}
diff --git a/sha1_file.c b/sha1_file.c
index 8734d501fe..43bc2ea0cf 100644
--- a/sha1_file.c
+++ b/sha1_file.c
@@ -684,26 +684,74 @@ static void *map_sha1_file_internal(const unsigned char *sha1,
 	return map;
 }
 
-static int unpack_sha1_header(z_stream *stream, void *map, unsigned long mapsize, void *buffer, unsigned long size)
+static int unpack_sha1_header(z_stream *stream, unsigned char *map, unsigned long mapsize, void *buffer, unsigned long bufsiz)
 {
+	unsigned char c;
+	unsigned int word, bits;
+	unsigned long size;
+	static const char *typename[8] = {
+		NULL,	/* OBJ_EXT */
+		"commit", "tree", "blob", "tag",
+		NULL, NULL, NULL
+	};
+	const char *type;
+
 	/* Get the data stream */
 	memset(stream, 0, sizeof(*stream));
 	stream->next_in = map;
 	stream->avail_in = mapsize;
 	stream->next_out = buffer;
-	stream->avail_out = size;
+	stream->avail_out = bufsiz;
+
+	/*
+	 * Is it a zlib-compressed buffer? If so, the first byte
+	 * must be 0x78 (15-bit window size, deflated), and the
+	 * first 16-bit word is evenly divisible by 31
+	 */
+	word = (map[0] << 8) + map[1];
+	if (map[0] == 0x78 && !(word % 31)) {
+		inflateInit(stream);
+		return inflate(stream, 0);
+	}
+
+	c = *map++;
+	mapsize--;
+	type = typename[(c >> 4) & 7];
+	if (!type)
+		return -1;
 
+	bits = 4;
+	size = c & 0xf;
+	while ((c & 0x80)) {
+		if (bits >= 8*sizeof(long))
+			return -1;
+		c = *map++;
+		size += (c & 0x7f) << bits;
+		bits += 7;
+		mapsize--;
+	}
+
+	/* Set up the stream for the rest.. */
+	stream->next_in = map;
+	stream->avail_in = mapsize;
 	inflateInit(stream);
-	return inflate(stream, 0);
+
+	/* And generate the fake traditional header */
+	stream->total_out = 1 + snprintf(buffer, bufsiz, "%s %lu", type, size);
+	return 0;
 }
 
 static void *unpack_sha1_rest(z_stream *stream, void *buffer, unsigned long size)
 {
 	int bytes = strlen(buffer) + 1;
 	unsigned char *buf = xmalloc(1+size);
+	unsigned long n;
 
-	memcpy(buf, (char *) buffer + bytes, stream->total_out - bytes);
-	bytes = stream->total_out - bytes;
+	n = stream->total_out - bytes;
+	if (n > size)
+		n = size;
+	memcpy(buf, (char *) buffer + bytes, n);
+	bytes = n;
 	if (bytes < size) {
 		stream->next_out = buf + bytes;
 		stream->avail_out = size - bytes;
@@ -1331,31 +1379,29 @@ char *write_sha1_file_prepare(void *buf,
 static int link_temp_to_file(const char *tmpfile, char *filename)
 {
 	int ret;
+	char *dir;
 
 	if (!link(tmpfile, filename))
 		return 0;
 
 	/*
-	 * Try to mkdir the last path component if that failed
-	 * with an ENOENT.
+	 * Try to mkdir the last path component if that failed.
 	 *
 	 * Re-try the "link()" regardless of whether the mkdir
 	 * succeeds, since a race might mean that somebody
 	 * else succeeded.
 	 */
 	ret = errno;
-	if (ret == ENOENT) {
-		char *dir = strrchr(filename, '/');
-		if (dir) {
-			*dir = 0;
-			mkdir(filename, 0777);
-			if (adjust_shared_perm(filename))
-				return -2;
-			*dir = '/';
-			if (!link(tmpfile, filename))
-				return 0;
-			ret = errno;
-		}
+	dir = strrchr(filename, '/');
+	if (dir) {
+		*dir = 0;
+		mkdir(filename, 0777);
+		if (adjust_shared_perm(filename))
+			return -2;
+		*dir = '/';
+		if (!link(tmpfile, filename))
+			return 0;
+		ret = errno;
 	}
 	return ret;
 }
@@ -1414,6 +1460,49 @@ static int write_buffer(int fd, const void *buf, size_t len)
 	return 0;
 }
 
+static int write_binary_header(unsigned char *hdr, enum object_type type, unsigned long len)
+{
+	int hdr_len;
+	unsigned char c;
+
+	c = (type << 4) | (len & 15);
+	len >>= 4;
+	hdr_len = 1;
+	while (len) {
+		*hdr++ = c | 0x80;
+		hdr_len++;
+		c = (len & 0x7f);
+		len >>= 7;
+	}
+	*hdr = c;
+	return hdr_len;
+}
+
+static void setup_object_header(z_stream *stream, const char *type, unsigned long len)
+{
+	int obj_type, hdr;
+
+	if (use_legacy_headers) {
+		while (deflate(stream, 0) == Z_OK)
+			/* nothing */;
+		return;
+	}
+	if (!strcmp(type, blob_type))
+		obj_type = OBJ_BLOB;
+	else if (!strcmp(type, tree_type))
+		obj_type = OBJ_TREE;
+	else if (!strcmp(type, commit_type))
+		obj_type = OBJ_COMMIT;
+	else if (!strcmp(type, tag_type))
+		obj_type = OBJ_TAG;
+	else
+		die("trying to generate bogus object of type '%s'", type);
+	hdr = write_binary_header(stream->next_out, obj_type, len);
+	stream->total_out = hdr;
+	stream->next_out += hdr;
+	stream->avail_out -= hdr;
+}
+
 int write_sha1_file(void *buf, unsigned long len, const char *type, unsigned char *returnsha1)
 {
 	int size;
@@ -1459,7 +1548,7 @@ int write_sha1_file(void *buf, unsigned long len, const char *type, unsigned cha
 	/* Set it up */
 	memset(&stream, 0, sizeof(stream));
 	deflateInit(&stream, zlib_compression_level);
-	size = deflateBound(&stream, len+hdrlen);
+	size = 8 + deflateBound(&stream, len+hdrlen);
 	compressed = xmalloc(size);
 
 	/* Compress it */
@@ -1469,8 +1558,7 @@ int write_sha1_file(void *buf, unsigned long len, const char *type, unsigned cha
 	/* First header.. */
 	stream.next_in = hdr;
 	stream.avail_in = hdrlen;
-	while (deflate(&stream, 0) == Z_OK)
-		/* nothing */;
+	setup_object_header(&stream, type, len);
 
 	/* Then the data itself.. */
 	stream.next_in = buf;
diff --git a/ssh-fetch.c b/ssh-fetch.c
index 28f7fd9174..6e16568f88 100644
--- a/ssh-fetch.c
+++ b/ssh-fetch.c
@@ -120,9 +120,10 @@ int fetch_ref(char *ref, unsigned char *sha1)
 
 static const char ssh_fetch_usage[] =
   MY_PROGRAM_NAME
-  " [-c] [-t] [-a] [-v] [-d] [--recover] [-w ref] commit-id url";
+  " [-c] [-t] [-a] [-v] [--recover] [-w ref] commit-id url";
 int main(int argc, char **argv)
 {
+	const char *write_ref = NULL;
 	char *commit_id;
 	char *url;
 	int arg = 1;
@@ -159,7 +160,6 @@ int main(int argc, char **argv)
 	}
 	commit_id = argv[arg];
 	url = argv[arg + 1];
-	write_ref_log_details = url;
 
 	if (setup_connection(&fd_in, &fd_out, prog, url, arg, argv + 1))
 		return 1;
@@ -167,7 +167,7 @@ int main(int argc, char **argv)
 	if (get_version())
 		return 1;
 
-	if (pull(commit_id))
+	if (pull(1, &commit_id, &write_ref, url))
 		return 1;
 
 	return 0;
diff --git a/t/t1400-update-ref.sh b/t/t1400-update-ref.sh
index 04fab26621..ddc80bbeae 100755
--- a/t/t1400-update-ref.sh
+++ b/t/t1400-update-ref.sh
@@ -14,6 +14,8 @@ D=4444444444444444444444444444444444444444
 E=5555555555555555555555555555555555555555
 F=6666666666666666666666666666666666666666
 m=refs/heads/master
+n_dir=refs/heads/gu
+n=$n_dir/fixes
 
 test_expect_success \
 	"create $m" \
@@ -26,6 +28,16 @@ test_expect_success \
 rm -f .git/$m
 
 test_expect_success \
+	"fail to create $n" \
+	'touch .git/$n_dir
+	 git-update-ref $n $A >out 2>err
+	 test $? = 1 &&
+	 test "" = "$(cat out)" &&
+	 grep "error: unable to resolve reference" err &&
+	 grep $n err'
+rm -f .git/$n_dir out err
+
+test_expect_success \
 	"create $m (by HEAD)" \
 	'git-update-ref HEAD $A &&
 	 test $A = $(cat .git/$m)'
diff --git a/t/t4102-apply-rename.sh b/t/t4102-apply-rename.sh
index fbb508d389..22da6a00cc 100755
--- a/t/t4102-apply-rename.sh
+++ b/t/t4102-apply-rename.sh
@@ -13,8 +13,8 @@ test_description='git-apply handling copy/rename patch.
 cat >test-patch <<\EOF
 diff --git a/foo b/bar
 similarity index 47%
-copy from foo
-copy to bar
+rename from foo
+rename to bar
 --- a/foo
 +++ b/bar
 @@ -1 +1 @@
@@ -39,4 +39,24 @@ else
 	    'test -f bar && ls -l bar | grep "^-..x......"'
 fi
 
+test_expect_success 'apply reverse' \
+    'git-apply -R --index --stat --summary --apply test-patch &&
+     test "$(cat foo)" = "This is foo"'
+
+cat >test-patch <<\EOF
+diff --git a/foo b/bar
+similarity index 47%
+copy from foo
+copy to bar
+--- a/foo
++++ b/bar
+@@ -1 +1 @@
+-This is foo
++This is bar
+EOF
+
+test_expect_success 'apply copy' \
+    'git-apply --index --stat --summary --apply test-patch &&
+     test "$(cat bar)" = "This is bar" -a "$(cat foo)" = "This is foo"'
+
 test_done
diff --git a/t/t4103-apply-binary.sh b/t/t4103-apply-binary.sh
index 00bd8b15c6..ff052699a2 100755
--- a/t/t4103-apply-binary.sh
+++ b/t/t4103-apply-binary.sh
@@ -35,8 +35,8 @@ git-commit -m 'Second Version'
 git-diff-tree -p master binary >B.diff
 git-diff-tree -p -C master binary >C.diff
 
-git-diff-tree -p --full-index master binary >BF.diff
-git-diff-tree -p --full-index -C master binary >CF.diff
+git-diff-tree -p --binary master binary >BF.diff
+git-diff-tree -p --binary -C master binary >CF.diff
 
 test_expect_success 'stat binary diff -- should not fail.' \
 	'git-checkout master
diff --git a/t/t4112-apply-renames.sh b/t/t4112-apply-renames.sh
index a06f6956d5..69e9603c78 100755
--- a/t/t4112-apply-renames.sh
+++ b/t/t4112-apply-renames.sh
@@ -11,31 +11,7 @@ test_description='git-apply should not get confused with rename/copy.
 
 # setup
 
-mkdir -p include/arch/x86_64/klibc klibc/arch/x86_64/include/klibc
-
-cat >include/arch/x86_64/klibc/archsetjmp.h <<\EOF
-/*
- * arch/x86_64/include/klibc/archsetjmp.h
- */
-
-#ifndef _KLIBC_ARCHSETJMP_H
-#define _KLIBC_ARCHSETJMP_H
-
-struct __jmp_buf {
-  unsigned long __rbx;
-  unsigned long __rsp;
-  unsigned long __rbp;
-  unsigned long __r12;
-  unsigned long __r13;
-  unsigned long __r14;
-  unsigned long __r15;
-  unsigned long __rip;
-};
-
-typedef struct __jmp_buf jmp_buf[1];
-
-#endif /* _SETJMP_H */
-EOF
+mkdir -p klibc/arch/x86_64/include/klibc
 
 cat >klibc/arch/x86_64/include/klibc/archsetjmp.h <<\EOF
 /*
@@ -139,7 +115,7 @@ rename to include/arch/m32r/klibc/archsetjmp.h
 +#endif /* _KLIBC_ARCHSETJMP_H */
 EOF
 
-find include klibc -type f -print | xargs git-update-index --add --
+find klibc -type f -print | xargs git-update-index --add --
 
 test_expect_success 'check rename/copy patch' 'git-apply --check patch'
 
diff --git a/t/t4114-apply-typechange.sh b/t/t4114-apply-typechange.sh
new file mode 100755
index 0000000000..ca81d72157
--- /dev/null
+++ b/t/t4114-apply-typechange.sh
@@ -0,0 +1,105 @@
+#!/bin/sh
+#
+# Copyright (c) 2006 Eric Wong
+#
+
+test_description='git-apply should not get confused with type changes.
+
+'
+
+. ./test-lib.sh
+
+test_expect_success 'setup repository and commits' '
+	echo "hello world" > foo &&
+	echo "hi planet" > bar &&
+	git update-index --add foo bar &&
+	git commit -m initial &&
+	git branch initial &&
+	rm -f foo &&
+	ln -s bar foo &&
+	git update-index foo &&
+	git commit -m "foo symlinked to bar" &&
+	git branch foo-symlinked-to-bar &&
+	rm -f foo &&
+	echo "how far is the sun?" > foo &&
+	git update-index foo &&
+	git commit -m "foo back to file" &&
+	git branch foo-back-to-file &&
+	rm -f foo &&
+	git update-index --remove foo &&
+	mkdir foo &&
+	echo "if only I knew" > foo/baz &&
+	git update-index --add foo/baz &&
+	git commit -m "foo becomes a directory" &&
+	git branch "foo-becomes-a-directory" &&
+	echo "hello world" > foo/baz &&
+	git update-index foo/baz &&
+	git commit -m "foo/baz is the original foo" &&
+	git branch foo-baz-renamed-from-foo
+	'
+
+test_expect_success 'file renamed from foo to foo/baz' '
+	git checkout -f initial &&
+	git diff-tree -M -p HEAD foo-baz-renamed-from-foo > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_expect_success 'file renamed from foo/baz to foo' '
+	git checkout -f foo-baz-renamed-from-foo &&
+	git diff-tree -M -p HEAD initial > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_expect_success 'directory becomes file' '
+	git checkout -f foo-becomes-a-directory &&
+	git diff-tree -p HEAD initial > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_expect_success 'file becomes directory' '
+	git checkout -f initial &&
+	git diff-tree -p HEAD foo-becomes-a-directory > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_expect_success 'file becomes symlink' '
+	git checkout -f initial &&
+	git diff-tree -p HEAD foo-symlinked-to-bar > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_expect_success 'symlink becomes file' '
+	git checkout -f foo-symlinked-to-bar &&
+	git diff-tree -p HEAD foo-back-to-file > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_expect_success 'symlink becomes directory' '
+	git checkout -f foo-symlinked-to-bar &&
+	git diff-tree -p HEAD foo-becomes-a-directory > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_expect_success 'directory becomes symlink' '
+	git checkout -f foo-becomes-a-directory &&
+	git diff-tree -p HEAD foo-symlinked-to-bar > patch &&
+	git apply --index < patch
+	'
+test_debug 'cat patch'
+
+
+test_done
diff --git a/t/t6004-rev-list-path-optim.sh b/t/t6004-rev-list-path-optim.sh
new file mode 100755
index 0000000000..5182dbb158
--- /dev/null
+++ b/t/t6004-rev-list-path-optim.sh
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+test_description='git-rev-list trivial path optimization test'
+
+. ./test-lib.sh
+
+test_expect_success setup '
+echo Hello > a &&
+git add a &&
+git commit -m "Initial commit" a
+'
+
+test_expect_success path-optimization '
+    commit=$(echo "Unchanged tree" | git-commit-tree "HEAD^{tree}" -p HEAD) &&
+    test $(git-rev-list $commit | wc -l) = 2 &&
+    test $(git-rev-list $commit -- . | wc -l) = 1
+'
+
+test_done
diff --git a/t/t7001-mv.sh b/t/t7001-mv.sh
index 811a4797a5..900ca93cde 100755
--- a/t/t7001-mv.sh
+++ b/t/t7001-mv.sh
@@ -38,4 +38,44 @@ test_expect_success \
     'git-diff-tree -r -M --name-status  HEAD^ HEAD | \
     grep -E "^R100.+path1/COPYING.+path0/COPYING"'
 
+test_expect_success \
+    'adding another file' \
+    'cp ../../README path0/README &&
+     git-add path0/README &&
+     git-commit -m add2 -a'
+
+test_expect_success \
+    'moving whole subdirectory' \
+    'git-mv path0 path2'
+
+test_expect_success \
+    'commiting the change' \
+    'git-commit -m dir-move -a'
+
+test_expect_success \
+    'checking the commit' \
+    'git-diff-tree -r -M --name-status  HEAD^ HEAD | \
+     grep -E "^R100.+path0/COPYING.+path2/COPYING" &&
+     git-diff-tree -r -M --name-status  HEAD^ HEAD | \
+     grep -E "^R100.+path0/README.+path2/README"'
+
+test_expect_success \
+    'moving whole subdirectory into subdirectory' \
+    'git-mv path2 path1'
+
+test_expect_success \
+    'commiting the change' \
+    'git-commit -m dir-move -a'
+
+test_expect_success \
+    'checking the commit' \
+    'git-diff-tree -r -M --name-status  HEAD^ HEAD | \
+     grep -E "^R100.+path2/COPYING.+path1/path2/COPYING" &&
+     git-diff-tree -r -M --name-status  HEAD^ HEAD | \
+     grep -E "^R100.+path2/README.+path1/path2/README"'
+
+test_expect_failure \
+    'do not move directory over existing directory' \
+    'mkdir path0 && mkdir path0/path2 && git-mv path2 path0'
+
 test_done
diff --git a/unpack-objects.c b/unpack-objects.c
index 3b824b04a2..48c1ee7968 100644
--- a/unpack-objects.c
+++ b/unpack-objects.c
@@ -241,11 +241,6 @@ static void unpack_one(unsigned nr, unsigned total)
 	}
 }
 
-/*
- * We unpack from the end, older files first. Now, usually
- * there are deltas etc, so we'll not actually write the
- * objects in that order, but we might as well try..
- */
 static void unpack_all(void)
 {
 	int i;
diff --git a/unpack-trees.c b/unpack-trees.c
new file mode 100644
index 0000000000..a20639be70
--- /dev/null
+++ b/unpack-trees.c
@@ -0,0 +1,799 @@
+#include <signal.h>
+#include <sys/time.h>
+#include "cache.h"
+#include "tree.h"
+#include "tree-walk.h"
+#include "cache-tree.h"
+#include "unpack-trees.h"
+
+#define DBRT_DEBUG 1
+
+struct tree_entry_list {
+	struct tree_entry_list *next;
+	unsigned directory : 1;
+	unsigned executable : 1;
+	unsigned symlink : 1;
+	unsigned int mode;
+	const char *name;
+	const unsigned char *sha1;
+};
+
+static struct tree_entry_list *create_tree_entry_list(struct tree *tree)
+{
+	struct tree_desc desc;
+	struct name_entry one;
+	struct tree_entry_list *ret = NULL;
+	struct tree_entry_list **list_p = &ret;
+
+	if (!tree->object.parsed)
+		parse_tree(tree);
+
+	desc.buf = tree->buffer;
+	desc.size = tree->size;
+
+	while (tree_entry(&desc, &one)) {
+		struct tree_entry_list *entry;
+
+		entry = xmalloc(sizeof(struct tree_entry_list));
+		entry->name = one.path;
+		entry->sha1 = one.sha1;
+		entry->mode = one.mode;
+		entry->directory = S_ISDIR(one.mode) != 0;
+		entry->executable = (one.mode & S_IXUSR) != 0;
+		entry->symlink = S_ISLNK(one.mode) != 0;
+		entry->next = NULL;
+
+		*list_p = entry;
+		list_p = &entry->next;
+	}
+	return ret;
+}
+
+static int entcmp(const char *name1, int dir1, const char *name2, int dir2)
+{
+	int len1 = strlen(name1);
+	int len2 = strlen(name2);
+	int len = len1 < len2 ? len1 : len2;
+	int ret = memcmp(name1, name2, len);
+	unsigned char c1, c2;
+	if (ret)
+		return ret;
+	c1 = name1[len];
+	c2 = name2[len];
+	if (!c1 && dir1)
+		c1 = '/';
+	if (!c2 && dir2)
+		c2 = '/';
+	ret = (c1 < c2) ? -1 : (c1 > c2) ? 1 : 0;
+	if (c1 && c2 && !ret)
+		ret = len1 - len2;
+	return ret;
+}
+
+static int unpack_trees_rec(struct tree_entry_list **posns, int len,
+			    const char *base, struct unpack_trees_options *o,
+			    int *indpos,
+			    struct tree_entry_list *df_conflict_list)
+{
+	int baselen = strlen(base);
+	int src_size = len + 1;
+	do {
+		int i;
+		const char *first;
+		int firstdir = 0;
+		int pathlen;
+		unsigned ce_size;
+		struct tree_entry_list **subposns;
+		struct cache_entry **src;
+		int any_files = 0;
+		int any_dirs = 0;
+		char *cache_name;
+		int ce_stage;
+
+		/* Find the first name in the input. */
+
+		first = NULL;
+		cache_name = NULL;
+
+		/* Check the cache */
+		if (o->merge && *indpos < active_nr) {
+			/* This is a bit tricky: */
+			/* If the index has a subdirectory (with
+			 * contents) as the first name, it'll get a
+			 * filename like "foo/bar". But that's after
+			 * "foo", so the entry in trees will get
+			 * handled first, at which point we'll go into
+			 * "foo", and deal with "bar" from the index,
+			 * because the base will be "foo/". The only
+			 * way we can actually have "foo/bar" first of
+			 * all the things is if the trees don't
+			 * contain "foo" at all, in which case we'll
+			 * handle "foo/bar" without going into the
+			 * directory, but that's fine (and will return
+			 * an error anyway, with the added unknown
+			 * file case.
+			 */
+
+			cache_name = active_cache[*indpos]->name;
+			if (strlen(cache_name) > baselen &&
+			    !memcmp(cache_name, base, baselen)) {
+				cache_name += baselen;
+				first = cache_name;
+			} else {
+				cache_name = NULL;
+			}
+		}
+
+#if DBRT_DEBUG > 1
+		if (first)
+			printf("index %s\n", first);
+#endif
+		for (i = 0; i < len; i++) {
+			if (!posns[i] || posns[i] == df_conflict_list)
+				continue;
+#if DBRT_DEBUG > 1
+			printf("%d %s\n", i + 1, posns[i]->name);
+#endif
+			if (!first || entcmp(first, firstdir,
+					     posns[i]->name,
+					     posns[i]->directory) > 0) {
+				first = posns[i]->name;
+				firstdir = posns[i]->directory;
+			}
+		}
+		/* No name means we're done */
+		if (!first)
+			return 0;
+
+		pathlen = strlen(first);
+		ce_size = cache_entry_size(baselen + pathlen);
+
+		src = xcalloc(src_size, sizeof(struct cache_entry *));
+
+		subposns = xcalloc(len, sizeof(struct tree_list_entry *));
+
+		if (cache_name && !strcmp(cache_name, first)) {
+			any_files = 1;
+			src[0] = active_cache[*indpos];
+			remove_cache_entry_at(*indpos);
+		}
+
+		for (i = 0; i < len; i++) {
+			struct cache_entry *ce;
+
+			if (!posns[i] ||
+			    (posns[i] != df_conflict_list &&
+			     strcmp(first, posns[i]->name))) {
+				continue;
+			}
+
+			if (posns[i] == df_conflict_list) {
+				src[i + o->merge] = o->df_conflict_entry;
+				continue;
+			}
+
+			if (posns[i]->directory) {
+				struct tree *tree = lookup_tree(posns[i]->sha1);
+				any_dirs = 1;
+				parse_tree(tree);
+				subposns[i] = create_tree_entry_list(tree);
+				posns[i] = posns[i]->next;
+				src[i + o->merge] = o->df_conflict_entry;
+				continue;
+			}
+
+			if (!o->merge)
+				ce_stage = 0;
+			else if (i + 1 < o->head_idx)
+				ce_stage = 1;
+			else if (i + 1 > o->head_idx)
+				ce_stage = 3;
+			else
+				ce_stage = 2;
+
+			ce = xcalloc(1, ce_size);
+			ce->ce_mode = create_ce_mode(posns[i]->mode);
+			ce->ce_flags = create_ce_flags(baselen + pathlen,
+						       ce_stage);
+			memcpy(ce->name, base, baselen);
+			memcpy(ce->name + baselen, first, pathlen + 1);
+
+			any_files = 1;
+
+			memcpy(ce->sha1, posns[i]->sha1, 20);
+			src[i + o->merge] = ce;
+			subposns[i] = df_conflict_list;
+			posns[i] = posns[i]->next;
+		}
+		if (any_files) {
+			if (o->merge) {
+				int ret;
+
+#if DBRT_DEBUG > 1
+				printf("%s:\n", first);
+				for (i = 0; i < src_size; i++) {
+					printf(" %d ", i);
+					if (src[i])
+						printf("%s\n", sha1_to_hex(src[i]->sha1));
+					else
+						printf("\n");
+				}
+#endif
+				ret = o->fn(src, o);
+
+#if DBRT_DEBUG > 1
+				printf("Added %d entries\n", ret);
+#endif
+				*indpos += ret;
+			} else {
+				for (i = 0; i < src_size; i++) {
+					if (src[i]) {
+						add_cache_entry(src[i], ADD_CACHE_OK_TO_ADD|ADD_CACHE_SKIP_DFCHECK);
+					}
+				}
+			}
+		}
+		if (any_dirs) {
+			char *newbase = xmalloc(baselen + 2 + pathlen);
+			memcpy(newbase, base, baselen);
+			memcpy(newbase + baselen, first, pathlen);
+			newbase[baselen + pathlen] = '/';
+			newbase[baselen + pathlen + 1] = '\0';
+			if (unpack_trees_rec(subposns, len, newbase, o,
+					     indpos, df_conflict_list))
+				return -1;
+			free(newbase);
+		}
+		free(subposns);
+		free(src);
+	} while (1);
+}
+
+/* Unlink the last component and attempt to remove leading
+ * directories, in case this unlink is the removal of the
+ * last entry in the directory -- empty directories are removed.
+ */
+static void unlink_entry(char *name)
+{
+	char *cp, *prev;
+
+	if (unlink(name))
+		return;
+	prev = NULL;
+	while (1) {
+		int status;
+		cp = strrchr(name, '/');
+		if (prev)
+			*prev = '/';
+		if (!cp)
+			break;
+
+		*cp = 0;
+		status = rmdir(name);
+		if (status) {
+			*cp = '/';
+			break;
+		}
+		prev = cp;
+	}
+}
+
+static volatile int progress_update = 0;
+
+static void progress_interval(int signum)
+{
+	progress_update = 1;
+}
+
+static void setup_progress_signal(void)
+{
+	struct sigaction sa;
+	struct itimerval v;
+
+	memset(&sa, 0, sizeof(sa));
+	sa.sa_handler = progress_interval;
+	sigemptyset(&sa.sa_mask);
+	sa.sa_flags = SA_RESTART;
+	sigaction(SIGALRM, &sa, NULL);
+
+	v.it_interval.tv_sec = 1;
+	v.it_interval.tv_usec = 0;
+	v.it_value = v.it_interval;
+	setitimer(ITIMER_REAL, &v, NULL);
+}
+
+static struct checkout state;
+static void check_updates(struct cache_entry **src, int nr,
+		struct unpack_trees_options *o)
+{
+	unsigned short mask = htons(CE_UPDATE);
+	unsigned last_percent = 200, cnt = 0, total = 0;
+
+	if (o->update && o->verbose_update) {
+		for (total = cnt = 0; cnt < nr; cnt++) {
+			struct cache_entry *ce = src[cnt];
+			if (!ce->ce_mode || ce->ce_flags & mask)
+				total++;
+		}
+
+		/* Don't bother doing this for very small updates */
+		if (total < 250)
+			total = 0;
+
+		if (total) {
+			fprintf(stderr, "Checking files out...\n");
+			setup_progress_signal();
+			progress_update = 1;
+		}
+		cnt = 0;
+	}
+
+	while (nr--) {
+		struct cache_entry *ce = *src++;
+
+		if (total) {
+			if (!ce->ce_mode || ce->ce_flags & mask) {
+				unsigned percent;
+				cnt++;
+				percent = (cnt * 100) / total;
+				if (percent != last_percent ||
+				    progress_update) {
+					fprintf(stderr, "%4u%% (%u/%u) done\r",
+						percent, cnt, total);
+					last_percent = percent;
+					progress_update = 0;
+				}
+			}
+		}
+		if (!ce->ce_mode) {
+			if (o->update)
+				unlink_entry(ce->name);
+			continue;
+		}
+		if (ce->ce_flags & mask) {
+			ce->ce_flags &= ~mask;
+			if (o->update)
+				checkout_entry(ce, &state, NULL);
+		}
+	}
+	if (total) {
+		signal(SIGALRM, SIG_IGN);
+		fputc('\n', stderr);
+	}
+}
+
+int unpack_trees(struct object_list *trees, struct unpack_trees_options *o)
+{
+	int indpos = 0;
+	unsigned len = object_list_length(trees);
+	struct tree_entry_list **posns;
+	int i;
+	struct object_list *posn = trees;
+	struct tree_entry_list df_conflict_list;
+	struct cache_entry df_conflict_entry;
+
+	memset(&df_conflict_list, 0, sizeof(df_conflict_list));
+	df_conflict_list.next = &df_conflict_list;
+	memset(&state, 0, sizeof(state));
+	state.base_dir = "";
+	state.force = 1;
+	state.quiet = 1;
+	state.refresh_cache = 1;
+
+	o->merge_size = len;
+	memset(&df_conflict_entry, 0, sizeof(df_conflict_entry));
+	o->df_conflict_entry = &df_conflict_entry;
+
+	if (len) {
+		posns = xmalloc(len * sizeof(struct tree_entry_list *));
+		for (i = 0; i < len; i++) {
+			posns[i] = create_tree_entry_list((struct tree *) posn->item);
+			posn = posn->next;
+		}
+		if (unpack_trees_rec(posns, len, o->prefix ? o->prefix : "",
+				     o, &indpos, &df_conflict_list))
+			return -1;
+	}
+
+	if (o->trivial_merges_only && o->nontrivial_merge)
+		die("Merge requires file-level merging");
+
+	check_updates(active_cache, active_nr, o);
+	return 0;
+}
+
+/* Here come the merge functions */
+
+static void reject_merge(struct cache_entry *ce)
+{
+	die("Entry '%s' would be overwritten by merge. Cannot merge.",
+	    ce->name);
+}
+
+static int same(struct cache_entry *a, struct cache_entry *b)
+{
+	if (!!a != !!b)
+		return 0;
+	if (!a && !b)
+		return 1;
+	return a->ce_mode == b->ce_mode &&
+		!memcmp(a->sha1, b->sha1, 20);
+}
+
+
+/*
+ * When a CE gets turned into an unmerged entry, we
+ * want it to be up-to-date
+ */
+static void verify_uptodate(struct cache_entry *ce,
+		struct unpack_trees_options *o)
+{
+	struct stat st;
+
+	if (o->index_only || o->reset)
+		return;
+
+	if (!lstat(ce->name, &st)) {
+		unsigned changed = ce_match_stat(ce, &st, 1);
+		if (!changed)
+			return;
+		errno = 0;
+	}
+	if (o->reset) {
+		ce->ce_flags |= htons(CE_UPDATE);
+		return;
+	}
+	if (errno == ENOENT)
+		return;
+	die("Entry '%s' not uptodate. Cannot merge.", ce->name);
+}
+
+static void invalidate_ce_path(struct cache_entry *ce)
+{
+	if (ce)
+		cache_tree_invalidate_path(active_cache_tree, ce->name);
+}
+
+/*
+ * We do not want to remove or overwrite a working tree file that
+ * is not tracked.
+ */
+static void verify_absent(const char *path, const char *action,
+		struct unpack_trees_options *o)
+{
+	struct stat st;
+
+	if (o->index_only || o->reset || !o->update)
+		return;
+	if (!lstat(path, &st))
+		die("Untracked working tree file '%s' "
+		    "would be %s by merge.", path, action);
+}
+
+static int merged_entry(struct cache_entry *merge, struct cache_entry *old,
+		struct unpack_trees_options *o)
+{
+	merge->ce_flags |= htons(CE_UPDATE);
+	if (old) {
+		/*
+		 * See if we can re-use the old CE directly?
+		 * That way we get the uptodate stat info.
+		 *
+		 * This also removes the UPDATE flag on
+		 * a match.
+		 */
+		if (same(old, merge)) {
+			*merge = *old;
+		} else {
+			verify_uptodate(old, o);
+			invalidate_ce_path(old);
+		}
+	}
+	else {
+		verify_absent(merge->name, "overwritten", o);
+		invalidate_ce_path(merge);
+	}
+
+	merge->ce_flags &= ~htons(CE_STAGEMASK);
+	add_cache_entry(merge, ADD_CACHE_OK_TO_ADD|ADD_CACHE_OK_TO_REPLACE);
+	return 1;
+}
+
+static int deleted_entry(struct cache_entry *ce, struct cache_entry *old,
+		struct unpack_trees_options *o)
+{
+	if (old)
+		verify_uptodate(old, o);
+	else
+		verify_absent(ce->name, "removed", o);
+	ce->ce_mode = 0;
+	add_cache_entry(ce, ADD_CACHE_OK_TO_ADD|ADD_CACHE_OK_TO_REPLACE);
+	invalidate_ce_path(ce);
+	return 1;
+}
+
+static int keep_entry(struct cache_entry *ce)
+{
+	add_cache_entry(ce, ADD_CACHE_OK_TO_ADD);
+	return 1;
+}
+
+#if DBRT_DEBUG
+static void show_stage_entry(FILE *o,
+			     const char *label, const struct cache_entry *ce)
+{
+	if (!ce)
+		fprintf(o, "%s (missing)\n", label);
+	else
+		fprintf(o, "%s%06o %s %d\t%s\n",
+			label,
+			ntohl(ce->ce_mode),
+			sha1_to_hex(ce->sha1),
+			ce_stage(ce),
+			ce->name);
+}
+#endif
+
+int threeway_merge(struct cache_entry **stages,
+		struct unpack_trees_options *o)
+{
+	struct cache_entry *index;
+	struct cache_entry *head;
+	struct cache_entry *remote = stages[o->head_idx + 1];
+	int count;
+	int head_match = 0;
+	int remote_match = 0;
+	const char *path = NULL;
+
+	int df_conflict_head = 0;
+	int df_conflict_remote = 0;
+
+	int any_anc_missing = 0;
+	int no_anc_exists = 1;
+	int i;
+
+	for (i = 1; i < o->head_idx; i++) {
+		if (!stages[i])
+			any_anc_missing = 1;
+		else {
+			if (!path)
+				path = stages[i]->name;
+			no_anc_exists = 0;
+		}
+	}
+
+	index = stages[0];
+	head = stages[o->head_idx];
+
+	if (head == o->df_conflict_entry) {
+		df_conflict_head = 1;
+		head = NULL;
+	}
+
+	if (remote == o->df_conflict_entry) {
+		df_conflict_remote = 1;
+		remote = NULL;
+	}
+
+	if (!path && index)
+		path = index->name;
+	if (!path && head)
+		path = head->name;
+	if (!path && remote)
+		path = remote->name;
+
+	/* First, if there's a #16 situation, note that to prevent #13
+	 * and #14.
+	 */
+	if (!same(remote, head)) {
+		for (i = 1; i < o->head_idx; i++) {
+			if (same(stages[i], head)) {
+				head_match = i;
+			}
+			if (same(stages[i], remote)) {
+				remote_match = i;
+			}
+		}
+	}
+
+	/* We start with cases where the index is allowed to match
+	 * something other than the head: #14(ALT) and #2ALT, where it
+	 * is permitted to match the result instead.
+	 */
+	/* #14, #14ALT, #2ALT */
+	if (remote && !df_conflict_head && head_match && !remote_match) {
+		if (index && !same(index, remote) && !same(index, head))
+			reject_merge(index);
+		return merged_entry(remote, index, o);
+	}
+	/*
+	 * If we have an entry in the index cache, then we want to
+	 * make sure that it matches head.
+	 */
+	if (index && !same(index, head)) {
+		reject_merge(index);
+	}
+
+	if (head) {
+		/* #5ALT, #15 */
+		if (same(head, remote))
+			return merged_entry(head, index, o);
+		/* #13, #3ALT */
+		if (!df_conflict_remote && remote_match && !head_match)
+			return merged_entry(head, index, o);
+	}
+
+	/* #1 */
+	if (!head && !remote && any_anc_missing)
+		return 0;
+
+	/* Under the new "aggressive" rule, we resolve mostly trivial
+	 * cases that we historically had git-merge-one-file resolve.
+	 */
+	if (o->aggressive) {
+		int head_deleted = !head && !df_conflict_head;
+		int remote_deleted = !remote && !df_conflict_remote;
+		/*
+		 * Deleted in both.
+		 * Deleted in one and unchanged in the other.
+		 */
+		if ((head_deleted && remote_deleted) ||
+		    (head_deleted && remote && remote_match) ||
+		    (remote_deleted && head && head_match)) {
+			if (index)
+				return deleted_entry(index, index, o);
+			else if (path)
+				verify_absent(path, "removed", o);
+			return 0;
+		}
+		/*
+		 * Added in both, identically.
+		 */
+		if (no_anc_exists && head && remote && same(head, remote))
+			return merged_entry(head, index, o);
+
+	}
+
+	/* Below are "no merge" cases, which require that the index be
+	 * up-to-date to avoid the files getting overwritten with
+	 * conflict resolution files.
+	 */
+	if (index) {
+		verify_uptodate(index, o);
+	}
+	else if (path)
+		verify_absent(path, "overwritten", o);
+
+	o->nontrivial_merge = 1;
+
+	/* #2, #3, #4, #6, #7, #9, #11. */
+	count = 0;
+	if (!head_match || !remote_match) {
+		for (i = 1; i < o->head_idx; i++) {
+			if (stages[i]) {
+				keep_entry(stages[i]);
+				count++;
+				break;
+			}
+		}
+	}
+#if DBRT_DEBUG
+	else {
+		fprintf(stderr, "read-tree: warning #16 detected\n");
+		show_stage_entry(stderr, "head   ", stages[head_match]);
+		show_stage_entry(stderr, "remote ", stages[remote_match]);
+	}
+#endif
+	if (head) { count += keep_entry(head); }
+	if (remote) { count += keep_entry(remote); }
+	return count;
+}
+
+/*
+ * Two-way merge.
+ *
+ * The rule is to "carry forward" what is in the index without losing
+ * information across a "fast forward", favoring a successful merge
+ * over a merge failure when it makes sense.  For details of the
+ * "carry forward" rule, please see <Documentation/git-read-tree.txt>.
+ *
+ */
+int twoway_merge(struct cache_entry **src,
+		struct unpack_trees_options *o)
+{
+	struct cache_entry *current = src[0];
+	struct cache_entry *oldtree = src[1], *newtree = src[2];
+
+	if (o->merge_size != 2)
+		return error("Cannot do a twoway merge of %d trees",
+			     o->merge_size);
+
+	if (current) {
+		if ((!oldtree && !newtree) || /* 4 and 5 */
+		    (!oldtree && newtree &&
+		     same(current, newtree)) || /* 6 and 7 */
+		    (oldtree && newtree &&
+		     same(oldtree, newtree)) || /* 14 and 15 */
+		    (oldtree && newtree &&
+		     !same(oldtree, newtree) && /* 18 and 19*/
+		     same(current, newtree))) {
+			return keep_entry(current);
+		}
+		else if (oldtree && !newtree && same(current, oldtree)) {
+			/* 10 or 11 */
+			return deleted_entry(oldtree, current, o);
+		}
+		else if (oldtree && newtree &&
+			 same(current, oldtree) && !same(current, newtree)) {
+			/* 20 or 21 */
+			return merged_entry(newtree, current, o);
+		}
+		else {
+			/* all other failures */
+			if (oldtree)
+				reject_merge(oldtree);
+			if (current)
+				reject_merge(current);
+			if (newtree)
+				reject_merge(newtree);
+			return -1;
+		}
+	}
+	else if (newtree)
+		return merged_entry(newtree, current, o);
+	else
+		return deleted_entry(oldtree, current, o);
+}
+
+/*
+ * Bind merge.
+ *
+ * Keep the index entries at stage0, collapse stage1 but make sure
+ * stage0 does not have anything there.
+ */
+int bind_merge(struct cache_entry **src,
+		struct unpack_trees_options *o)
+{
+	struct cache_entry *old = src[0];
+	struct cache_entry *a = src[1];
+
+	if (o->merge_size != 1)
+		return error("Cannot do a bind merge of %d trees\n",
+			     o->merge_size);
+	if (a && old)
+		die("Entry '%s' overlaps.  Cannot bind.", a->name);
+	if (!a)
+		return keep_entry(old);
+	else
+		return merged_entry(a, NULL, o);
+}
+
+/*
+ * One-way merge.
+ *
+ * The rule is:
+ * - take the stat information from stage0, take the data from stage1
+ */
+int oneway_merge(struct cache_entry **src,
+		struct unpack_trees_options *o)
+{
+	struct cache_entry *old = src[0];
+	struct cache_entry *a = src[1];
+
+	if (o->merge_size != 1)
+		return error("Cannot do a oneway merge of %d trees",
+			     o->merge_size);
+
+	if (!a)
+		return deleted_entry(old, old, o);
+	if (old && same(old, a)) {
+		if (o->reset) {
+			struct stat st;
+			if (lstat(old->name, &st) ||
+			    ce_match_stat(old, &st, 1))
+				old->ce_flags |= htons(CE_UPDATE);
+		}
+		return keep_entry(old);
+	}
+	return merged_entry(a, old, o);
+}
diff --git a/unpack-trees.h b/unpack-trees.h
new file mode 100644
index 0000000000..c4601621cd
--- /dev/null
+++ b/unpack-trees.h
@@ -0,0 +1,35 @@
+#ifndef UNPACK_TREES_H
+#define UNPACK_TREES_H
+
+struct unpack_trees_options;
+
+typedef int (*merge_fn_t)(struct cache_entry **src,
+		struct unpack_trees_options *options);
+
+struct unpack_trees_options {
+	int reset;
+	int merge;
+	int update;
+	int index_only;
+	int nontrivial_merge;
+	int trivial_merges_only;
+	int verbose_update;
+	int aggressive;
+	const char *prefix;
+	merge_fn_t fn;
+
+	int head_idx;
+	int merge_size;
+
+	struct cache_entry *df_conflict_entry;
+};
+
+extern int unpack_trees(struct object_list *trees,
+		struct unpack_trees_options *options);
+
+int threeway_merge(struct cache_entry **stages, struct unpack_trees_options *o);
+int twoway_merge(struct cache_entry **src, struct unpack_trees_options *o);
+int bind_merge(struct cache_entry **src, struct unpack_trees_options *o);
+int oneway_merge(struct cache_entry **src, struct unpack_trees_options *o);
+
+#endif
diff --git a/upload-pack.c b/upload-pack.c
index f6f5a7e3db..07ecdb4281 100644
--- a/upload-pack.c
+++ b/upload-pack.c
@@ -182,6 +182,8 @@ static void create_pack_file(void)
 		ssize_t sz;
 		int pe, pu, pollsize;
 
+		reset_timeout();
+
 		pollsize = 0;
 		pe = pu = -1;