diff --git a/Documentation/git-clone.txt b/Documentation/git-clone.txt
index 985043faca..874934a332 100644
--- a/Documentation/git-clone.txt
+++ b/Documentation/git-clone.txt
@@ -11,8 +11,7 @@ SYNOPSIS
 [verse]
 'git-clone' [--template=<template_directory>] [-l [-s]] [-q] [-n] [--bare]
 	  [-o <name>] [-u <upload-pack>] [--reference <repository>]
-	  [--use-separate-remote | --no-separate-remote] <repository>
-	  [<directory>]
+	  <repository> [<directory>]
 
 DESCRIPTION
 -----------
@@ -99,18 +98,6 @@ OPTIONS
 	if unset the templates are taken from the installation
 	defined default, typically `/usr/share/git-core/templates`.
 
---use-separate-remote::
-	Save remotes heads under `$GIT_DIR/remotes/origin/` instead
-	of `$GIT_DIR/refs/heads/`.  Only the local master branch is
-	saved in the latter. This is the default.
-
---no-separate-remote::
-	Save remotes heads in the same namespace as the local
-	heads, `$GIT_DIR/refs/heads/'.  In regular repositories,
-	this is a legacy setup git-clone created by default in
-	older Git versions, and will be removed before the next
-	major release.
-
 <repository>::
 	The (possibly remote) repository to clone from.  It can
 	be any URL git-fetch supports.
diff --git a/Documentation/git-merge-file.txt b/Documentation/git-merge-file.txt
new file mode 100644
index 0000000000..0b41d66a70
--- /dev/null
+++ b/Documentation/git-merge-file.txt
@@ -0,0 +1,92 @@
+git-merge-file(1)
+============
+
+NAME
+----
+git-merge-file - threeway file merge
+
+
+SYNOPSIS
+--------
+[verse]
+'git-merge-file' [-L <current-name> [-L <base-name> [-L <other-name>]]]
+	[-p|--stdout] [-q|--quiet] <current-file> <base-file> <other-file>
+
+
+DESCRIPTION
+-----------
+git-file-merge incorporates all changes that lead from the `<base-file>`
+to `<other-file>` into `<current-file>`. The result ordinarily goes into
+`<current-file>`. git-merge-file is useful for combining separate changes
+to an original. Suppose `<base-file>` is the original, and both
+`<current-file>` and `<other-file>` are modifications of `<base-file>`.
+Then git-merge-file combines both changes.
+
+A conflict occurs if both `<current-file>` and `<other-file>` have changes
+in a common segment of lines. If a conflict is found, git-merge-file
+normally outputs a warning and brackets the conflict with <<<<<<< and
+>>>>>>> lines. A typical conflict will look like this:
+
+	<<<<<<< A
+	lines in file A
+	=======
+	lines in file B
+	>>>>>>> B
+
+If there are conflicts, the user should edit the result and delete one of
+the alternatives.
+
+The exit value of this program is negative on error, and the number of
+conflicts otherwise. If the merge was clean, the exit value is 0.
+
+git-merge-file is designed to be a minimal clone of RCS merge, that is, it
+implements all of RCS merge's functionality which is needed by
+gitlink:git[1].
+
+
+OPTIONS
+-------
+
+-L <label>::
+	This option may be given up to three times, and
+	specifies labels to be used in place of the
+	corresponding file names in conflict reports. That is,
+	`git-merge-file -L x -L y -L z a b c` generates output that
+	looks like it came from files x, y and z instead of
+	from files a, b and c.
+
+-p::
+	Send results to standard output instead of overwriting
+	`<current-file>`.
+
+-q::
+	Quiet;  do  not  warn about conflicts.
+
+
+EXAMPLES
+--------
+
+git merge-file README.my README README.upstream::
+
+	combines the changes of README.my and README.upstream since README,
+	tries to merge them and writes the result into README.my.
+
+git merge-file -L a -L b -L c tmp/a123 tmp/b234 tmp/c345::
+
+	merges tmp/a123 and tmp/c345 with the base tmp/b234, but uses labels
+	`a` and `c` instead of `tmp/a123` and `tmp/c345`.
+
+
+Author
+------
+Written by Johannes Schindelin <johannes.schindelin@gmx.de>
+
+
+Documentation
+--------------
+Documentation by Johannes Schindelin and the git-list <git@vger.kernel.org>,
+with parts copied from the original documentation of RCS merge.
+
+GIT
+---
+Part of the gitlink:git[7] suite
diff --git a/Documentation/git.txt b/Documentation/git.txt
index 6382ef0a02..2a9e97dac1 100644
--- a/Documentation/git.txt
+++ b/Documentation/git.txt
@@ -351,6 +351,9 @@ gitlink:git-init-db[1]::
 	Creates an empty git object database, or reinitialize an
 	existing one.
 
+gitlink:git-merge-file[1]::
+	Runs a threeway merge.
+
 gitlink:git-merge-index[1]::
 	Runs a merge for files needing merging.
 
diff --git a/git-clone.sh b/git-clone.sh
index 992cb7c0cc..f37eb9d105 100755
--- a/git-clone.sh
+++ b/git-clone.sh
@@ -14,7 +14,7 @@ die() {
 }
 
 usage() {
-	die "Usage: $0 [--template=<template_directory>] [--no-separate-remote] [--reference <reference-repo>] [--bare] [-l [-s]] [-q] [-u <upload-pack>] [--origin <name>] [--depth <n>] [-n] <repo> [<dir>]"
+	die "Usage: $0 [--template=<template_directory>] [--reference <reference-repo>] [--bare] [-l [-s]] [-q] [-u <upload-pack>] [--origin <name>] [--depth <n>] [-n] <repo> [<dir>]"
 }
 
 get_repo_base() {
@@ -138,11 +138,9 @@ while
 	*,--template=*)
 	  template="$1" ;;
 	*,-q|*,--quiet) quiet=-q ;;
-	*,--use-separate-remote)
-		# default
-		use_separate_remote=t ;;
+	*,--use-separate-remote) ;;
 	*,--no-separate-remote)
-		use_separate_remote= ;;
+		die "clones are always made with separate-remote layout" ;;
 	1,--reference) usage ;;
 	*,--reference)
 		shift; reference="$1" ;;
@@ -340,12 +338,8 @@ cd "$D" || exit
 
 if test -z "$bare" && test -f "$GIT_DIR/REMOTE_HEAD"
 then
-	# Figure out which remote branch HEAD points at.
-	case "$use_separate_remote" in
-	'')	remote_top=refs/heads ;;
-	*)	remote_top="refs/remotes/$origin" ;;
-	esac
-
+	# a non-bare repository is always in separate-remote layout
+	remote_top="refs/remotes/$origin"
 	head_sha1=`cat "$GIT_DIR/REMOTE_HEAD"`
 	case "$head_sha1" in
 	'ref: refs/'*)
@@ -379,41 +373,26 @@ then
 		)
 	)
 
-	# Write out remotes/$origin file, and update our "$head_points_at".
+	# Write out remote.$origin config, and update our "$head_points_at".
 	case "$head_points_at" in
 	?*)
-		mkdir -p "$GIT_DIR/remotes" &&
+		# Local default branch
 		git-symbolic-ref HEAD "refs/heads/$head_points_at" &&
-		case "$use_separate_remote" in
-		t)	origin_track="$remote_top/$head_points_at"
-			git-update-ref HEAD "$head_sha1" ;;
-		*)	origin_track="$remote_top/$origin"
-			git-update-ref "refs/heads/$origin" "$head_sha1" ;;
-		esac &&
+
+		# Tracking branch for the primary branch at the remote.
+		origin_track="$remote_top/$head_points_at" &&
+		git-update-ref HEAD "$head_sha1" &&
+
+		# Upstream URL
 		git-repo-config remote."$origin".url "$repo" &&
+
+		# Set up the mappings to track the remote branches.
 		git-repo-config remote."$origin".fetch \
-			"refs/heads/$head_points_at:$origin_track" &&
-		(cd "$GIT_DIR/$remote_top" && find . -type f -print) |
-		while read dotslref
-		do
-			name=`expr "$dotslref" : './\(.*\)'`
-			if test "z$head_points_at" = "z$name"
-			then
-				continue
-			fi
-			if test "$use_separate_remote" = '' &&
-			   test "z$origin" = "z$name"
-			then
-				continue
-			fi
-			git-repo-config remote."$origin".fetch "refs/heads/${name}:$remote_top/${name}" '^$'
-		done &&
-		case "$use_separate_remote" in
-		t)
-			rm -f "refs/remotes/$origin/HEAD"
-			git-symbolic-ref "refs/remotes/$origin/HEAD" \
-				"refs/remotes/$origin/$head_points_at"
-		esac &&
+			"refs/heads/*:$remote_top/*" '^$' &&
+		rm -f "refs/remotes/$origin/HEAD"
+		git-symbolic-ref "refs/remotes/$origin/HEAD" \
+			"refs/remotes/$origin/$head_points_at" &&
+
 		git-repo-config branch."$head_points_at".remote "$origin" &&
 		git-repo-config branch."$head_points_at".merge "refs/heads/$head_points_at"
 	esac
diff --git a/git-merge.sh b/git-merge.sh
index 1f01a08e4e..a17aa2c86e 100755
--- a/git-merge.sh
+++ b/git-merge.sh
@@ -136,6 +136,22 @@ merge_local_changes () {
 	)
 }
 
+merge_name () {
+	remote="$1"
+	rh=$(git-rev-parse --verify "$remote^0" 2>/dev/null) || return
+	bh=$(git-show-ref -s --verify "refs/heads/$remote" 2>/dev/null)
+	if test "$rh" = "$bh"
+	then
+		echo "$rh		branch '$remote' of ."
+	elif truname=$(expr "$remote" : '\(.*\)~[1-9][0-9]*$') &&
+		git-show-ref -q --verify "refs/heads/$truname" 2>/dev/null
+	then
+		echo "$rh		branch '$truname' (early part) of ."
+	else
+		echo "$rh		commit '$remote'"
+	fi
+}
+
 case "$#" in 0) usage ;; esac
 
 rloga= have_message=
@@ -233,15 +249,7 @@ else
 	# in this loop.
 	merge_name=$(for remote
 		do
-			rh=$(git-rev-parse --verify "$remote"^0 2>/dev/null) ||
-			continue ;# not something we can merge
-			bh=$(git show-ref -s --verify "refs/heads/$remote" 2>/dev/null)
-			if test "$rh" = "$bh"
-			then
-				echo "$rh		branch '$remote' of ."
-			else
-				echo "$rh		commit '$remote'"
-			fi
+			merge_name "$remote"
 		done | git-fmt-merge-msg
 	)
 	merge_msg="${merge_msg:+$merge_msg$LF$LF}$merge_name"
diff --git a/git-parse-remote.sh b/git-parse-remote.sh
index 6ae534bf89..f27c3c231b 100755
--- a/git-parse-remote.sh
+++ b/git-parse-remote.sh
@@ -144,7 +144,8 @@ canon_refs_list_for_fetch () {
 			curr_branch=$(git-symbolic-ref HEAD | \
 			    sed -e 's|^refs/heads/||')
 			merge_branches=$(git-repo-config \
-			    --get-all "branch.${curr_branch}.merge")
+			    --get-all "branch.${curr_branch}.merge") ||
+			merge_branches=.this.would.never.match.any.ref.
 		fi
 		set x $(expand_refs_wildcard "$@")
 		shift
diff --git a/wt-status.c b/wt-status.c
index c388ce1293..cface6ca88 100644
--- a/wt-status.c
+++ b/wt-status.c
@@ -271,7 +271,7 @@ static void wt_status_print_verbose(struct wt_status *s)
 
 void wt_status_print(struct wt_status *s)
 {
-	if (s->branch && strcmp(s->branch, "refs/heads/master"))
+	if (s->branch)
 		color_printf_ln(color(WT_STATUS_HEADER),
 			"# On branch %s", s->branch);