Setup the default remote and merge config in CloneCommand

Bug: 336621
Change-Id: I8c889d7b42f6f121d096acad1fada8e3752d74f9
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>

org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java

 import org.eclipse.jgit.dircache.DirCacheCheckout;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ProgressMonitor;
 
 /**
  * Clone a repository into a new working directory
- * 
+ *
  * @see <a href="http://www.kernel.org/pub/software/scm/git/docs/git-clone.html"
  *      >Git documentation about Clone</a>
  */
 
 		config.addFetchRefSpec(refSpec);
 		config.update(repo.getConfig());
+
+		repo.getConfig().setString(ConfigConstants.CONFIG_BRANCH_SECTION,
+				branch, ConfigConstants.CONFIG_REMOTE_SECTION, remote);
+		repo.getConfig().setString(ConfigConstants.CONFIG_BRANCH_SECTION,
+				branch, ConfigConstants.CONFIG_KEY_MERGE, branch); //$NON-NLS-1$ //$NON-NLS-2$
+
 		repo.getConfig().save();
 
 		// run the fetch command