diff --git a/Documentation/RelNotes-1.6.3.1.txt b/Documentation/RelNotes-1.6.3.1.txt
new file mode 100644
index 0000000000..2400b72ef7
--- /dev/null
+++ b/Documentation/RelNotes-1.6.3.1.txt
@@ -0,0 +1,10 @@
+GIT v1.6.3.1 Release Notes
+==========================
+
+Fixes since v1.6.3
+------------------
+
+* "git checkout -b new-branch" with a staged change in the index
+  incorrectly primed the in-index cache-tree, resulting a wrong tree
+  object to be written out of the index.  This is a grave regression
+  since the last 1.6.2.X maintenance release.
diff --git a/Documentation/git-clone.txt b/Documentation/git-clone.txt
index 4072f40d7a..b14de6c407 100644
--- a/Documentation/git-clone.txt
+++ b/Documentation/git-clone.txt
@@ -149,7 +149,7 @@ then the cloned repository will become corrupt.
 	part of the source repository is used if no directory is
 	explicitly given ("repo" for "/path/to/repo.git" and "foo"
 	for "host.xz:foo/.git").  Cloning into an existing directory
-	is not allowed.
+	is only allowed if the directory is empty.
 
 :git-clone: 1
 include::urls.txt[]
diff --git a/Documentation/git-config.txt b/Documentation/git-config.txt
index 7131ee3c66..f68b198205 100644
--- a/Documentation/git-config.txt
+++ b/Documentation/git-config.txt
@@ -69,7 +69,8 @@ OPTIONS
 
 --add::
 	Adds a new line to the option without altering any existing
-	values.  This is the same as providing '^$' as the value_regex.
+	values.  This is the same as providing '^$' as the value_regex
+	in `--replace-all`.
 
 --get::
 	Get the value for a given key (optionally filtered by a regex
@@ -155,7 +156,7 @@ See also <<FILES>>.
 	When the color setting for `name` is undefined, the command uses
 	`color.ui` as fallback.
 
---get-color name default::
+--get-color name [default]::
 
 	Find the color configured for `name` (e.g. `color.diff.new`) and
 	output it as the ANSI color escape sequence to the standard
diff --git a/GIT-VERSION-GEN b/GIT-VERSION-GEN
index 39cde784c9..d292e3a2d3 100755
--- a/GIT-VERSION-GEN
+++ b/GIT-VERSION-GEN
@@ -1,7 +1,7 @@
 #!/bin/sh
 
 GVF=GIT-VERSION-FILE
-DEF_VER=v1.6.3.GIT
+DEF_VER=v1.6.3.1
 
 LF='
 '
diff --git a/RelNotes b/RelNotes
index dd8bc4bb4a..0f6a588f1d 120000
--- a/RelNotes
+++ b/RelNotes
@@ -1 +1 @@
-Documentation/RelNotes-1.6.3.txt
\ No newline at end of file
+Documentation/RelNotes-1.6.3.1.txt
\ No newline at end of file
diff --git a/archive-tar.c b/archive-tar.c
index ba890ebdec..cee06ce3cb 100644
--- a/archive-tar.c
+++ b/archive-tar.c
@@ -180,7 +180,7 @@ static int write_tar_entry(struct archiver_args *args,
 
 	sprintf(header.mode, "%07o", mode & 07777);
 	sprintf(header.size, "%011lo", S_ISREG(mode) ? size : 0);
-	sprintf(header.mtime, "%011lo", args->time);
+	sprintf(header.mtime, "%011lo", (unsigned long) args->time);
 
 	sprintf(header.uid, "%07o", 0);
 	sprintf(header.gid, "%07o", 0);
diff --git a/builtin-checkout.c b/builtin-checkout.c
index 15f0c32c7a..dc4bfb5fc0 100644
--- a/builtin-checkout.c
+++ b/builtin-checkout.c
@@ -365,17 +365,14 @@ static int merge_working_tree(struct checkout_opts *opts,
 	int ret;
 	struct lock_file *lock_file = xcalloc(1, sizeof(struct lock_file));
 	int newfd = hold_locked_index(lock_file, 1);
-	int reprime_cache_tree = 0;
 
 	if (read_cache() < 0)
 		return error("corrupt index file");
 
-	cache_tree_free(&active_cache_tree);
 	if (opts->force) {
 		ret = reset_tree(new->commit->tree, opts, 1);
 		if (ret)
 			return ret;
-		reprime_cache_tree = 1;
 	} else {
 		struct tree_desc trees[2];
 		struct tree *tree;
@@ -411,9 +408,7 @@ static int merge_working_tree(struct checkout_opts *opts,
 		init_tree_desc(&trees[1], tree->buffer, tree->size);
 
 		ret = unpack_trees(2, trees, &topts);
-		if (ret != -1) {
-			reprime_cache_tree = 1;
-		} else {
+		if (ret == -1) {
 			/*
 			 * Unpack couldn't do a trivial merge; either
 			 * give up or do a real merge, depending on
@@ -457,8 +452,6 @@ static int merge_working_tree(struct checkout_opts *opts,
 		}
 	}
 
-	if (reprime_cache_tree)
-		prime_cache_tree(&active_cache_tree, new->commit->tree);
 	if (write_cache(newfd, active_cache, active_nr) ||
 	    commit_locked_index(lock_file))
 		die("unable to write new index file");
diff --git a/git-merge-one-file.sh b/git-merge-one-file.sh
index e1eb963266..9c2c1b7202 100755
--- a/git-merge-one-file.sh
+++ b/git-merge-one-file.sh
@@ -113,6 +113,10 @@ case "${1:-.}${2:-.}${3:-.}" in
 	src1=`git-unpack-file $2`
 	git merge-file "$src1" "$orig" "$src2"
 	ret=$?
+	msg=
+	if [ $ret -ne 0 ]; then
+		msg='content conflict'
+	fi
 
 	# Create the working tree file, using "our tree" version from the
 	# index, and then store the result of the merge.
@@ -120,7 +124,10 @@ case "${1:-.}${2:-.}${3:-.}" in
 	rm -f -- "$orig" "$src1" "$src2"
 
 	if [ "$6" != "$7" ]; then
-		echo "ERROR: Permissions conflict: $5->$6,$7."
+		if [ -n "$msg" ]; then
+			msg="$msg, "
+		fi
+		msg="${msg}permissions conflict: $5->$6,$7"
 		ret=1
 	fi
 	if [ "$1" = '' ]; then
@@ -128,7 +135,7 @@ case "${1:-.}${2:-.}${3:-.}" in
 	fi
 
 	if [ $ret -ne 0 ]; then
-		echo "ERROR: Merge conflict in $4"
+		echo "ERROR: $msg in $4"
 		exit 1
 	fi
 	exec git update-index -- "$4"
diff --git a/t/t2014-switch.sh b/t/t2014-switch.sh
new file mode 100755
index 0000000000..ccfb147113
--- /dev/null
+++ b/t/t2014-switch.sh
@@ -0,0 +1,28 @@
+#!/bin/sh
+
+test_description='Peter MacMillan'
+. ./test-lib.sh
+
+test_expect_success setup '
+	echo Hello >file &&
+	git add file &&
+	test_tick &&
+	git commit -m V1 &&
+	echo Hello world >file &&
+	git add file &&
+	git checkout -b other
+'
+
+test_expect_success 'check all changes are staged' '
+	git diff --exit-code
+'
+
+test_expect_success 'second commit' '
+	git commit -m V2
+'
+
+test_expect_success 'check' '
+	git diff --cached --exit-code
+'
+
+test_done