For VS2010 and before I was utilizing Web Deployment Projects (WDP) to help package my website for production deployment. I had a MSBuild script that compiled the solution in r
It appears that there are now some other options for publishing from the command-line. Specifically something along the lines of the following seems possible now with some RC updates to Visual Studio 2012.
msbuild mywap.csproj /p:DeployOnBuild=true;PublishProfile=MyProfileName
For more details check out this post by Scott Hanselman and check out the section on Publishing.
I wasn't able to get the publish to run, but looking at the output from Visual Studio I think I have found an alternate solution. Turns out the obj\Release\AspnetCompileMerge folder has a deployable and clean version of the project. It contains byte identical files to the final output folder.
I did have to change my msbuild script to include the DeployOnBuild option...
<MSBuild Properties="Configuration=Release;DeployOnBuild=True;"
StopOnFirstFailure="true"
Projects="$(BuildDirectory)\BigWave.ALL.sln"></MSBuild>