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_is_managed() in install_shared_infra now consults manifest.is_recovered() before treating a hash-matching file as managed. Files marked recovered (pre-existing on disk, not installed by Spec Kit) are no longer overwritten by integration use/switch even when their hash matches the manifest entry. This closes the gap documented in the manifest API: callers using refresh_managed MUST check is_recovered first. Co-authored-by: Manfred Riem <mnriem@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>