The onboarding step S4_AgentMdStep.java:40-48 loads the agent prompt with this fallback order:

AGENT.private.md — the real runtime file (written after onboarding completes, contains the user's personalized prompt)
AGENT.md — first fallback (template with placeholders)
AGENT-ORIGINAL.md — second fallback (identical template, "backup")
AGENT-ORIGINAL.md exists as a safety net so that if the user edits/deletes AGENT.md before completing onboarding, the original template is still available. But since AGENT.md is tracked in git, this scenario is unlikely — and the fallback chain already ends with an empty string anyway.

You can safely drop AGENT-ORIGINAL.md. The two-level fallback (AGENT.md → AGENT-ORIGINAL.md) is redundant since they have the same content and AGENT.md serves as the template just fine.

You'd just need to remove the one line at S4_AgentMdStep.java:45 and then delete the AGENT-ORIGINAL.MD