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Looking at the docs, the automation API seems to assume writing/reading to the `Pulumi..yaml`.  You can try passing an explicit `workDir` in the options, e.g. `/tmp`

<https://www.pulumi.com/docs/reference/pkg/nodejs/pulumi/pulumi/automation/#LocalWorkspaceOptions-workDir>

Which, tracing through the code from `setAllConfig` the answer seems to be because the automation api is simply wrapping the pulumi cli <https://github.com/pulumi/pulumi/blob/72d48f162e7d6f288a5c5e5944ec90ce483824a5/sdk/nodejs/automation/cmd.ts#L55>

<https://github.com/pulumi/pulumi/blob/72d48f162e7d6f288a5c5e5944ec90ce483824a5/sdk/nodejs/automation/localWorkspace.ts#L416-L424>