I have a c# ClickOnce application that I need to be able to publish multiple times for OEM purposes.
The way I understand it now is that publish settings are located
I found that you are able to edit certain properties using MSBuild.exe like this
MSBuild Solution.sln /target:publish /property:ProductName=ProductA\;Publisher=CompanyA\;ApplicationIcon=companyA.ico
I found another useful post on modifying.csproj files programatically with .NET code. (This would only be needed if you're modifying things that are deeper than just the project properties specified in the ClickOnce documentation below)
The MSBuild documentation here was also useful -- especially under Publishing Properties