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1. Yes we will bundle the config files (there are two now, mapViewerConfig.xml plus the new mds.xml file) and upload them to OTN for download in the next couple days. In the mean time you can unzip the mapviewer.ear and the web.war file inside it to a temp folder, then copy the two .xml files from the WEB-INF/conf/ directory to the folder of your choice.
2. We will fix the doc with regard to the reference of -Djava.awt.headless; but it sounded like you were able to add the -Doracle.maps.config option to that file. To verify if this option was actually picked up and used by mapViewer, you can log into mapViewer's admin console, click Management then Configuration. On top of the configuration data, there is a File Location field which shows where the mapViewerConfig.xml file is being loaded.
5. The new mapviewer.ear no longer ships any tutorial/demo/sample request or online API docs; all of those are now packaged into the separately deploy-able MVDEMO application (which you can download from the same OTN mapviewer site since version 188.8.131.52.1). This was mentioned in the 184.108.40.206 release note (http://download.oracle.com/otndocs/products/mapviewer/mapviewer_11p6_readme.txt).
6. Please refer to 1 above about needing both .xml files (mds.xml and mapViewerConfig.xml) for mapviewer to function properly.