When a seam project is generated and run on the embedded eap server, if you delete the .war or the -ds from the deploy directory, Dev Studio doesn't handle it properly.

The Dev Studio seems to push only a delta of changed files to the server, and doesn't check to see if the war has been tampered or removed. So if you now attempt to "Run on Server", it will fail as there will be no .war file deployed. Changing one of the files in the project, saving it, then hitting "Run On Server" again results in the changed file being pushed to a .war in the server's deploy directory, but nothing else.

I managed to get Dev Studio to push the whole project to the server by restarting Dev Studio.