I originally added this to QB-2369, but got no response.

After an upgrade from 6.1.19 to 6.1.20, I'm getting:

2016-07-14 05:10:51,480 [qtp1006161290-49] ERROR com.pmease.quickbuild.repositorysupport.Repository - Error constructing repository from DOM.
 java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
  at com.pmease.quickbuild.bootstrap.BootstrapUtils.wrapAsUnchecked(BootstrapUtils.java:56)
  at com.pmease.quickbuild.util.ExceptionUtils.wrapAsUnchecked(ExceptionUtils.java:82)
  at com.pmease.quickbuild.migration.MigrationHelper.migrate(MigrationHelper.java:158)
  at com.pmease.quickbuild.migration.VersionedDocument.toBean(VersionedDocument.java:531)
  at com.pmease.quickbuild.migration.VersionedDocument.toBean(VersionedDocument.java:500)
  at com.pmease.quickbuild.repositorysupport.Repository.fromDOM(Repository.java:704)
  at com.pmease.quickbuild.model.Configuration.getRepositories(Configuration.java:2027)
  at com.pmease.quickbuild.model.Configuration.findRepositories(Configuration.java:1932)
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:498)
  at org.hibernate.proxy.pojo.javassist.JavassistLazyInitializer.invoke(JavassistLazyInitializer.java:196)
  at com.pmease.quickbuild.model.Configuration_$$_jvstc42_0.findRepositories(Configuration_$$_jvstc42_0.java)
  at com.pmease.quickbuild.web.page.setting.RepositoriesPanel$8.iterator(RepositoriesPanel.java:282)
  at org.apache.wicket.markup.repeater.data.DataViewBase$ModelIterator.<init>(DataViewBase.java:109)
  at org.apache.wicket.markup.repeater.data.DataViewBase.getItemModels(DataViewBase.java:76)
  at org.apache.wicket.markup.repeater.AbstractPageableView.getItemModels(AbstractPageableView.java:101)
  at org.apache.wicket.markup.repeater.RefreshingView.onPopulate(RefreshingView.java:93)
  at org.apache.wicket.markup.repeater.AbstractRepeater.onBeforeRender(AbstractRepeater.java:119)
  at org.apache.wicket.markup.repeater.AbstractPageableView.onBeforeRender(AbstractPageableView.java:115)
  at org.apache.wicket.Component.internalBeforeRender(Component.java:986)
  at org.apache.wicket.Component.beforeRender(Component.java:1022)
  at org.apache.wicket.MarkupContainer.onBeforeRenderChildren(MarkupContainer.java:1785)
  at org.apache.wicket.Component.onBeforeRender(Component.java:3798)
  at org.apache.wicket.Component.internalBeforeRender(Component.java:986)
  at org.apache.wicket.Component.beforeRender(Component.java:1022)
  at org.apache.wicket.MarkupContainer.onBeforeRenderChildren(MarkupContainer.java:1785)
  at org.apache.wicket.Component.onBeforeRender(Component.java:3798)
  at org.apache.wicket.Component.internalBeforeRender(Component.java:986)
  at org.apache.wicket.Component.beforeRender(Component.java:1022)
  at org.apache.wicket.MarkupContainer.onBeforeRenderChildren(MarkupContainer.java:1785)
  at org.apache.wicket.Component.onBeforeRender(Component.java:3798)
  at org.apache.wicket.Component.internalBeforeRender(Component.java:986)
  at org.apache.wicket.Component.beforeRender(Component.java:1022)
  at org.apache.wicket.MarkupContainer.onBeforeRenderChildren(MarkupContainer.java:1785)
  at org.apache.wicket.Component.onBeforeRender(Component.java:3798)
  at org.apache.wicket.Component.internalBeforeRender(Component.java:986)
  at org.apache.wicket.Component.beforeRender(Component.java:1022)
  at org.apache.wicket.MarkupContainer.onBeforeRenderChildren(MarkupContainer.java:1785)
  at org.apache.wicket.Component.onBeforeRender(Component.java:3798)
  at org.apache.wicket.Page.onBeforeRender(Page.java:823)
  at com.pmease.quickbuild.web.page.BasePage.onBeforeRender(BasePage.java:345)
  at org.apache.wicket.Component.internalBeforeRender(Component.java:986)
  at org.apache.wicket.Component.beforeRender(Component.java:1022)
  at org.apache.wicket.Component.internalPrepareForRender(Component.java:2191)
  at org.apache.wicket.Page.internalPrepareForRender(Page.java:280)
  at org.apache.wicket.Component.render(Component.java:2280)
  at org.apache.wicket.Page.renderPage(Page.java:1035)
  at org.apache.wicket.request.handler.render.WebPageRenderer.renderPage(WebPageRenderer.java:105)
  at org.apache.wicket.request.handler.render.WebPageRenderer.respond(WebPageRenderer.java:182)
  at org.apache.wicket.request.handler.RenderPageRequestHandler.respond(RenderPageRequestHandler.java:147)
  at org.apache.wicket.request.cycle.RequestCycle$HandlerExecutor.respond(RequestCycle.java:719)
  at org.apache.wicket.request.RequestHandlerStack.execute(RequestHandlerStack.java:63)
  at org.apache.wicket.request.cycle.RequestCycle.processRequest(RequestCycle.java:210)
  at org.apache.wicket.request.cycle.RequestCycle.processRequestAndDetach(RequestCycle.java:253)
  at org.apache.wicket.protocol.http.WicketFilter.processRequest(WicketFilter.java:162)
  at org.apache.wicket.protocol.http.WicketServlet.doGet(WicketServlet.java:137)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:734)
  at com.pmease.quickbuild.web.MainServlet.service(MainServlet.java:133)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
  at org.eclipse.equinox.http.helper.FilterServletAdaptor$FilterChainImpl.doFilter(FilterServletAdaptor.java:56)
  at org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:82)
  at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:243)
  at org.eclipse.equinox.http.helper.FilterServletAdaptor.service(FilterServletAdaptor.java:37)
  at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:669)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1336)
  at com.pmease.quickbuild.Quickbuild$DisableTraceFilter.doFilter(Quickbuild.java:1057)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1307)
  at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:453)
  at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
  at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1072)
  at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:382)
  at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
  at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1006)
  at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
  at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:154)
  at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
  at org.eclipse.jetty.server.Server.handle(Server.java:365)
  at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:485)
  at org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
  at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:926)
  at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:988)
  at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:635)
  at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
  at org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
  at org.eclipse.jetty.server.bio.SocketConnector$ConnectorEndPoint.run(SocketConnector.java:264)
  at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
  at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
  at java.lang.Thread.run(Thread.java:745)
 Caused by: java.lang.reflect.InvocationTargetException
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:498)
  at com.pmease.quickbuild.migration.MigrationHelper.migrate(MigrationHelper.java:156)
  ... 87 more
 Caused by: org.dom4j.IllegalAddException: The node "org.dom4j.tree.DefaultElement@7f3af4d9 [Element: <contextLabel attributes: []/>]" could not be added to the branch "null" because: Cannot add another element to this Document as it already has a root element of: com.pmease.quickbuild.plugin.scm.github.GitHubRepository
  at org.dom4j.tree.AbstractDocument.checkAddElementAllowed(AbstractDocument.java:241)
  at org.dom4j.tree.AbstractDocument.add(AbstractDocument.java:203)
  at org.dom4j.tree.AbstractDocument.addElement(AbstractDocument.java:173)
  at com.pmease.quickbuild.migration.VersionedDocument.addElement(VersionedDocument.java:205)
  at com.pmease.quickbuild.plugin.scm.github.GitHubRepository.migrate1(GitHubRepository.java:294)
  ... 92 more