Agent refuses to use shell/bash under any circumstance

Bug Description
Agent refuses to use shell commands under any circumstance, citing a system prompt preventing agent use of shell tools. This breaks any workflow where shell access would be needed (most of them!). I tried this on 2.1.58 and 2.1.71. Same issue with both.

Environment Info

• Platform: darwin
• Terminal: Apple_Terminal
• Version: 2.1.58 and 2.1.71
• Feedback ID: 2e056617-d60b-4aaf-9516-622e7b26b5ed

Errors

[{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n    at CQT (/$bunfs/root/claude:1809:15122)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:36.276Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server greptile invalid: Missing environment variables: GREPTILE_API_KEY\n    at CQT (/$bunfs/root/claude:1809:15122)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:36.276Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n    at CQT (/$bunfs/root/claude:1809:15122)\n    at async X (/$bunfs/root/claude:4088:15587)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.223Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server greptile invalid: Missing environment variables: GREPTILE_API_KEY\n    at CQT (/$bunfs/root/claude:1809:15122)\n    at async X (/$bunfs/root/claude:4088:15587)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.223Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n    at CQT (/$bunfs/root/claude:1809:15122)\n    at async L (/$bunfs/root/claude:4088:16120)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.223Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server greptile invalid: Missing environment variables: GREPTILE_API_KEY\n    at CQT (/$bunfs/root/claude:1809:15122)\n    at async L (/$bunfs/root/claude:4088:16120)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.223Z"},{"error":"Error: LSP server plugin:kotlin-lsp:kotlin-lsp failed to start: Executable not found in $PATH: \"kotlin-lsp\"\n    at start (/$bunfs/root/claude:2638:22314)\n    at async H (/$bunfs/root/claude:2638:24624)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.247Z"},{"error":"Error: LSP server plugin:typescript-lsp:typescript failed to start: Executable not found in $PATH: \"typescript-language-server\"\n    at start (/$bunfs/root/claude:2638:22314)\n    at async H (/$bunfs/root/claude:2638:24624)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.247Z"},{"error":"Error: LSP server plugin:pyright-lsp:pyright failed to start: Executable not found in $PATH: \"pyright-langserver\"\n    at start (/$bunfs/root/claude:2638:22314)\n    at async H (/$bunfs/root/claude:2638:24624)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.247Z"},{"error":"Error: Executable not found in $PATH: \"kotlin-lsp\"\n    at spawn (unknown)\n    at spawn (node:child_process:667:35)\n    at spawn (node:child_process:14:39)\n    at start (/$bunfs/root/claude:2638:20844)\n    at H (/$bunfs/root/claude:2638:24624)\n    at _ (/$bunfs/root/claude:2638:32726)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-03-08T10:24:37.247Z"},{"error":"Error: Executable not found in $PATH: \"typescript-language-server\"\n    at spawn (unknown)\n    at spawn (node:child_pr…

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