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Claude Code and Qoder reject permission-bypass flags when the process runs as root (EUID 0). This causes the agent to crash with exit status 1, and the nil agentSession triggers a panic in the engine's interactive message handler. For Claude Code: downgrade bypassPermissions mode to auto (which auto-approves permissions internally in cc-connect, avoiding the CLI flag entirely). For Qoder: skip --dangerously-skip-permissions under root. Both log a warning so the user knows why YOLO mode is degraded. Closes #1054