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Hey @BenNewman100, thanks for this question.

They're layers, not competing philosophies: deterministic CLI commands handle state and bookkeeping (status, instructions, archive) to keep agents on the rails, while skills drive the agent through the judgment work, and spec merging turned out to be judgment work, since a fully deterministic merge was tried (#1279/#1288) and proved too brittle in practice. That's why merging lives with the agent today, and it's also why your transient-context markup idea in #678 is appealing: the agent writes the final wording at authoring time when it has the context, leaving only a mechanical strip for sync.

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@BenNewman100
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