diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
index b9bc25857..ae1c5d9fe 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
@@ -150,4 +150,34 @@ public class MockSystemReader extends SystemReader {
 	public Locale getLocale() {
 		return Locale.US;
 	}
+
+	/**
+	 * Assign some properties for the currently executing platform
+	 */
+	public void setCurrentPlatform() {
+		setProperty("os.name", System.getProperty("os.name"));
+		setProperty("file.separator", System.getProperty("file.separator"));
+		setProperty("path.separator", System.getProperty("path.separator"));
+		setProperty("line.separator", System.getProperty("line.separator"));
+	}
+
+	/**
+	 * Emulate Windows
+	 */
+	public void setWindows() {
+		setProperty("os.name", "Windows");
+		setProperty("file.separator", "\\");
+		setProperty("path.separator", ";");
+		setProperty("line.separator", "\r\n");
+	}
+
+	/**
+	 * Emulate Unix
+	 */
+	public void setUnix() {
+		setProperty("os.name", "*nix"); // Essentially anything but Windows
+		setProperty("file.separator", "/");
+		setProperty("path.separator", ":");
+		setProperty("line.separator", "\n");
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
index c7a30ebe1..85686da4d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
@@ -46,6 +46,7 @@ package org.eclipse.jgit.api;
 import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
@@ -122,6 +123,7 @@ public class MergeCommand extends GitCommand<MergeResult> {
 									Integer.valueOf(commits.size())));
 
 		RevWalk revWalk = null;
+		DirCacheCheckout dco = null;
 		try {
 			Ref head = repo.getRef(Constants.HEAD);
 			if (head == null)
@@ -147,7 +149,7 @@ public class MergeCommand extends GitCommand<MergeResult> {
 			ObjectId headId = head.getObjectId();
 			if (headId == null) {
 				revWalk.parseHeaders(srcCommit);
-				DirCacheCheckout dco = new DirCacheCheckout(repo,
+				dco = new DirCacheCheckout(repo,
 						repo.lockDirCache(), srcCommit.getTree());
 				dco.setFailOnConflict(true);
 				dco.checkout();
@@ -176,7 +178,7 @@ public class MergeCommand extends GitCommand<MergeResult> {
 				// FAST_FORWARD detected: skip doing a real merge but only
 				// update HEAD
 				refLogMessage.append(": " + MergeStatus.FAST_FORWARD);
-				DirCacheCheckout dco = new DirCacheCheckout(repo,
+				dco = new DirCacheCheckout(repo,
 						headCommit.getTree(), repo.lockDirCache(),
 						srcCommit.getTree());
 				dco.setFailOnConflict(true);
@@ -214,7 +216,7 @@ public class MergeCommand extends GitCommand<MergeResult> {
 				refLogMessage.append(mergeStrategy.getName());
 				refLogMessage.append('.');
 				if (noProblems) {
-					DirCacheCheckout dco = new DirCacheCheckout(repo,
+					dco = new DirCacheCheckout(repo,
 							headCommit.getTree(), repo.lockDirCache(),
 							merger.getResultTreeId());
 					dco.setFailOnConflict(true);
@@ -250,6 +252,10 @@ public class MergeCommand extends GitCommand<MergeResult> {
 					}
 				}
 			}
+		} catch (org.eclipse.jgit.errors.CheckoutConflictException e) {
+			List<String> conflicts = (dco == null) ? Collections
+					.<String> emptyList() : dco.getConflicts();
+			throw new CheckoutConflictException(conflicts, e);
 		} catch (IOException e) {
 			throw new JGitInternalException(
 					MessageFormat.format(
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/CheckoutConflictException.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/CheckoutConflictException.java
index de45c1d8e..4d5bd1e03 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/CheckoutConflictException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/CheckoutConflictException.java
@@ -48,6 +48,20 @@ public class CheckoutConflictException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 	private List<String> conflictingPaths;
 
+	/**
+	 * Translate internal exception to API exception
+	 *
+	 * @param conflictingPaths
+	 *            list of conflicting paths
+	 *
+	 * @param e
+	 */
+	public CheckoutConflictException(List<String> conflictingPaths,
+			org.eclipse.jgit.errors.CheckoutConflictException e) {
+		super(e.getMessage(), e);
+		this.conflictingPaths = conflictingPaths;
+	}
+
 	CheckoutConflictException(String message, Throwable cause) {
 		super(message, cause);
 	}
@@ -73,6 +87,7 @@ public class CheckoutConflictException extends GitAPIException {
 
 	/**
 	 * Adds a new conflicting path
+	 *
 	 * @param conflictingPath
 	 * @return {@code this}
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java b/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java
index e8263c5a9..f66e5e7ef 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java
@@ -232,7 +232,9 @@ public class PlotCommitList<L extends PlotLane> extends
 			if (newPos == -1)
 				newPos = positionsAllocated++;
 			freePositions.add(commit.lane.getPosition());
+			activeLanes.remove(commit.lane);
 			commit.lane.position = newPos;
+			activeLanes.add(commit.lane);
 		}
 	}
 
diff --git a/tools/version.sh b/tools/version.sh
index 2fae5e142..eaff9a61d 100755
--- a/tools/version.sh
+++ b/tools/version.sh
@@ -141,7 +141,7 @@ perl -pi~ -e '
 		$seen_version = 0;
 		$old_argv = $ARGV;
 	}
-	if ($seen_version < 6) {
+	if ($seen_version < 5) {
 		$seen_version++ if
 		s{<(version)>.*</\1>}{<${1}>'"$POM_V"'</${1}>};
 	}