No there is no way to install an MDS Studio application via the desktop manager.
Nope, there is no way to make a .cod or .jad out of the jar in the repository either.
The MDS Runtime applications (MDS Studio or VS.NET plugin) must be deployed to a BES and installed via the BES administrator pushing the app down to the device or the user installing the app from the MDS Control Center
All communications go through the MDS Services so even if you connected the blackberry via the USB cable the communications would be sent through the MDS Services. So your Web Service on the local machine would need to be visible on your computer to your LAN.
You could make this all happen even if the device isn't connected to your PC. You could simply put some autentication on your web service and the device will get a challenge response.
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