Fly.toml config not being used

[ignoramous]

@martylamb

But if I run fly config display or fly config env I see no env vars at all.

Are you deploying a regular Fly app or Fly Machines? If the latter, try fly m status <machine-id> -d -a <app-name>. A list of active Machines can be fetched via fly m list -a <app-name>