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diff --git a/tests.branching/merge.script b/tests.branching/merge.script
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+#!/bin/sh
+# Copyright (C) 2012  Codethink Limited
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; version 2 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+# Check that "morph merge" merges a system branch into master
+
+set -eu
+
+# Create system branch.
+cd "$DATADIR/workspace"
+"$SRCDIR/scripts/test-morph" init
+"$SRCDIR/scripts/test-morph" branch baserock:morphs baserock/newbranch
+
+# Make a change to a chunk.
+"$SRCDIR/scripts/test-morph" edit hello-system hello-stratum hello
+cd baserock/newbranch/baserock:hello
+touch newfile.txt
+git add newfile.txt
+git commit -m foo --quiet
+
+# Commit in morphs repo
+cd ../baserock:morphs
+git commit --all --quiet -m "Update morph refs for baserock/newbranch"
+
+# Merge changes back to master
+cd "$DATADIR/workspace"
+"$SRCDIR/scripts/test-morph" checkout baserock:morphs master
+cd master
+"$SRCDIR/scripts/test-morph" merge baserock/newbranch
+
+# Check results.
+cd baserock:hello
+git status --short # make sure all changes are committed
+[ -e newfile.txt ] # make sure the new file is there
+
+# Make sure all refs to the merged branch have gone.
+cd ../baserock:morphs
+! grep "\"ref\": \"baserock/newbranch\"" *.morph