When publishing from Nuke, does Ayon save the workfile right at the start of the publish and put it aside into temp?
No it’s saved early during extraction, see here.
Why?
Note that pyblish plug-ins should be implemented in a way that publishing is idempotent (exactly the same behavior when republishing) by having the publish system not alter the user’s scene state. So theoretically it should not be relevant at which time it’s saved, as long as it is anywhere during the publish.
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