There's no reference to my current project in the stack (dev.json) I just deployed. Where is project metadata stored (if at all) when using an s3 backend with the automation API?

You can use a local backend and then explore the files. It’s the same as S3.

Right - but my question still stands - how is project metadata placed in a custom backend (s3 or local)? In my bucket I see directories for stacks, backups, and history

Sorry I misunderstood the specifics of what you were asking. Yes that is a known current limitation of all of the file-state backends. See here: https://github.com/pulumi/pulumi/issues/2522 In Pulumi SaaS stack names are unique to the project. In file-state backends stack names are globally unique.

Thanks for the link. It's easy enough to workaround this (i.e. prepending the project name)