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Added Zotero item deletion handling: repository history is retained when items move to trash and cleaned only after permanent deletion or trash emptying.
Added a git4zotero/index.json repository index to map Zotero items, attachments, and local version repositories.
Added preference-pane orphan history checks and cleanup for legacy unmanaged repository directories.
Added safety checks so cleanup only removes plugin repositories whose paths and metadata match the deleted Zotero item.