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Is it possible to set different entry points for different stacks? I was hoping you could just set "main" to a different entry in the stack yaml file but it appears not

You could grab something from stack config and just branch to a different actual main function based on that. Doesn't feel like something that really needs an extra feature to do.

Is it possible to list all the stacks within a project without using the command line?

Have you looked at the automation api? https://www.pulumi.com/docs/guides/automation-api/