What do you mean by config files get combined? When I deploy from C2, there is a config.xml file under the www folder. There is also one in the directory above www that does not seem to be updating so I assume this is from me exporting in the old format at some point. Are you saying i need to copy the file from the www folder to the root? Also, are you putting '*' in the Intent and Navigation boxes?
I am not having any success trying different things. Any help is greatly appreciated!