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pkg update now shares the planner the system-module refresh uses: a module disabled or hand-pinned in the local vault is left alone, a developer's own directory or linked build is never replaced, and any module that could not be updated makes the command fail. The superseded store copy is still collected.
A refresh now plans under Recover, UpdateAll or UpdateNamed and returns a typed skip reason. A bulk update skips modules missing from the registry and versions installed from an explicit artifact instead of failing; naming a module overrides an inferred pin and fails with a hint when it is disabled or not store-managed. Versions a refresh already collected no longer count as a hand pin, so a registry rollback can't leave a module stuck. The update fetches the registry fresh, reads the local vault strictly, logs each change and tells the user to run apply, and pkg update is documented.
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