I don't see it in the .sln file, which is what I expected.
Which project is the "startup" project only has any relevance for debugging, which means it's user metadata from the point of the solution and the projects. Regardless of which project is the "startup" project, the compiled code is the same.
Because of this, the information is stored as a user setting in the Solution User Options file (solution.suo) which accompanies the Solution file (solution.sln). The .suo file "Records all of the options that you might associate with your solution so that each time you open it, it includes customizations that you have made" according to MSDN.
The .suo file is a binary file. If you want to read or change it programatically, you have to use IVsPersistSolutionOpts.LoadUserOptions
from the Microsoft.VisualStudio.Shell.Interop
namespace.
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