yes, we are working on making the distinction between the two deployment types (and lack of control for manual deployed items) more clear in the console.

/ike

On Apr 23, 2012, at 10:16 PM, Brian Stansberry wrote:

An important thing to realize with the scanner though is if you use the 
scanner, your API for managing those deployments becomes the OS's 
filesystem API. Users shouldn't try to then manipulate the deployments 
via the CLI or console. The web console isn't going to let you update or 
remove the deployments -- you need to manipulate the deployments/ dir.