Nidhideep,
The SMP3 server starting with SP04 supports multiple Agentry applications on the same server. As such, when uploading it will not go into the C:\SAP\MobilePlatform3\Server\configuration\com.sap.mobile.platform.server.agentry.application folder but instead to the application specific folder that is created based on the app id you entered in the cockpit. In your case the C:\SAP\MobilePlatform3\Server\configuration\com.sap.mobile.platform.server.agentry.application.SAPWM folder.
As a production Agentry application, the Agentry.ini and some of the other configuration files are stored in the persistence database and not in the filesystem. This is the normal behavior under SMP3.
After publishing restart either the Agentry Application through the cockpit or the SMP3 instance and try to connect to the URL.
--Bill