A startup script runs once, as root, the first time a server boots.
Choose Orchestration › Startup Scripts and add a script. Start it with a #! line, and keep it under 64 KB.
When you deploy, pick it under Advanced › Startup script.
Editing a script doesn't change servers already built with it; the next ones get the new version. For cloud-init, use the Cloud-init user data box on the Deploy page instead.
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