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Three bugs fixed: 1. Deduplicate run messages when same run appears in both linkedRuns and liveRuns during transition, preventing assistant-ui MessageRepository crash. 2. Render waitingText as content in live run messages so empty transcript doesn't produce an empty chat bubble. 3. Auto-initialize git repo in agent home directories so Claude Code doesn't reject the workspace as untrusted. Co-Authored-By: Paperclip <noreply@paperclip.ing>