Configure permissions changedpermissions
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443443If your organization has set a [claude.ai connector](/docs/en/mcp#organization-controls-on-connector-tools) tool to `ask`, allow rules for that tool don't take effect: Claude Code prompts on every call, even in `auto` and `bypassPermissions` modes. In `dontAsk` mode, which never prompts, Claude Code denies the call instead. Connector tools appear as `mcp__claude_ai_<server>__<tool>`.
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445In a [Cowork](https://claude.com/docs/cowork/overview) session in the Claude Desktop app, Claude runs shell commands through Cowork's `mcp__workspace__bash` tool rather than the built-in `Bash` tool, and Cowork likewise provides `mcp__workspace__web_fetch` for web fetches. Claude Code also applies deny rules that name the whole `Bash` or `WebFetch` tool to these Cowork tools, so a managed `Bash` deny rule stops Claude from running shell commands in Cowork. When Claude Code blocks such a call, the message names the Cowork tool: `Permission to use mcp__workspace__bash has been denied.` Allow rules don't carry over: Claude Code never applies a `Bash` allow rule to `mcp__workspace__bash`.
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445447### Agent (subagents)
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447449Use `Agent(AgentName)` rules to control which [subagents](/docs/en/sub-agents) Claude can use:
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