Ok, finally figured this out.
The command line you need is:
msbuild path/to/your/webdirectory/YourWeb.csproj /p:Configuration=Debug;DeployOnBuild=True;PackageAsSingleFile=False
You can change where the project outputs to by adding a property of outdir=c:\wherever\ in the /p: section.
This will create the output at:
path/to/your/webdirectory/obj/Debug/Package/PackageTmp/
You can then copy those files from the above directory using whatever method you’d like.
I’ve got this all working as a ruby rake task using Albacore. I am trying to get it all done so I can actually put it as a contribution to the project. But if anyone wants the code before that, let me know.
Another wrinkle I found was that it was putting in Tokenized Parameters into the Web.config. If you don’t need that feature, make sure you add:
/p:AutoParameterizationWebConfigConnectionStrings=false