Claude Code Security: Why Permission Modes and Sandbox Boundaries Must Work Together

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A technical breakdown of Claude Code's security architecture highlights how teams often conflate permission modes with sandbox boundaries, leading to dangerous misconfigurations. Permission modes — Auto, Prompt, Restricted, and Custom — determine whether Claude attempts an action, while sandbox tools like bubblewrap and Seatbelt define what those actions can access if executed. The --allowedTools whitelist blocks specific capabilities such as run_command or edit_file but does not restrict file paths or network access within permitted tools. For example, allowing run_command without a restricted sandbox directory can let the agent execute destructive commands like rm -rf / unchecked. A defense-in-depth approach that pairs explicit permission deny rules with tight sandbox restrictions is recommended to prevent a single misconfiguration from compromising an entire system.

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