More than two (:-)) folks asked this question recently so it might worth a short note. The question is how does one deploy a new mapviewer version (e.g. 126.96.36.199.1) into the quickstart kit (which has 188.8.131.52.0)? A manual process is the simplest.
Shutdown the glassfish server if it's running.
Make a copy of the existing mapviewer.war directory and rename it (e.g. mapviewer.war.111170).
Delete the contents of the mapviewer.war directory (or create one named mapviewer.war if you just renamed, without copying, the old one).
Extract the contents of web.war in the new mapviewer.ear into the mapviewer.war directory.
Modify the mapviewerconfig.xml file so that it has the same map_data_source and other entries as the original one had.
If you're replacing 184.108.40.206.0 with 220.127.116.11.1 then you also have to edit the mds.xml (same location as mapviewerconfig.xml) to allow for the streaming of predefined and dynamic themes to the html5 client by the map data serevr. This change (data server streaming disabled by default) is new in 18.104.22.168.1.