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Revises the Codex native manifests plan to reflect a mid-implementation correction: the Bun converter's --to codex default is now agents-only, with an --include-skills opt-in for standalone installs. The original plan framed agents as "out of scope," which missed that the two-step flow only works cleanly when the converter's default complements native install rather than duplicating it. Also flags that the entire --to codex converter path is expected to be deprecated once Codex's native plugin spec supports custom agents.