Roo reset all controller .java files (deleting all handwritten code) after command "web mvc all --package com.xyz.package

I executed following command.

>web mvc all --package com.softrism.tortlets.web

It reset all my java controller files (yes, java not aj) as if I did not have any custom code ! Attached snapshot of my IDE. Good that i have checked in everything repository. But still had lot of unchecked code !! Also, it deleted all my json controller ITDs. I think it should have kept those intact as well.

Couple of things I had done before executing command so that problem might help reproducing.
1- Had deleted RooToString annotiation from all entities.
2 - Had run "web json all" command. (to get restful services)
3- Had added custom logic for json based methods (those also disappeared)
4- Had changed some update.jspx(reset with z="?") so that Roo regenerates those entries.( it was not generating as expected, so i tried the above command).
5- Had setup rest-shell to test json api and was using with the server.