devenv MySetUpproject.vdproj /rebuild
and u get a new setup.msi and setup.exe.
what i'm currently doing is using a batch file to do this
this is my complete batch file
D:
cd D:\Program Files\Microsoft Visual Studio 9.0\Common7\IDE\
devenv %1\Service.sln /project "Setup\Setup.vdproj" /projectconfig Release /rebuild
I'm setting the path to my devenv folder and then calling the devenv exe from command line using a parameter sent to the batch file (%1). :)..since we are giving a switch devenv wont open and build the project from the command line itself.