I'm also having problems using Run As, although I don't have any duplicate gws.xml files. I'm not sure what happened. The only change I have made is to add a new plugin to eclipse called IdafeUml. I suppose this could have caused a problem, but it seems really unlikely. Before when I used Run As/Compile or Run As/Application everything worked, now I get no action whatsoever. Nothing happens!
Please let me know what I can do. I think my computer's version of Java may have been updated too.