[Bug] Bypass permissions mode overrides user tool preferences in CLAUDE.md and MCP tools

Bug Description
Title: Bypass permissions mode should not change which tools the model uses What happens: When bypass permissions mode is on, Claude Code adds this text to the model's instructions: ▎ "You can do much of your work through the Bash tool when it is the simpler route: read files with cat, head, or sed -n, search with grep and find, and make small, mechanical file changes with sed, heredocs, or short scripts instead of the dedicated Read, Edit, or Write tools." The text is softer than an earlier version, which said "Do your work through the Bash tool wherever it can accomplish the job". It still pushes the model toward grep and find. Why this is a problem: - A permission mode should control prompts, not tool choice. I use bypass mode only so that long autonomous builds do not stop to ask me. I did not ask for a different way of working. - My CLAUDE.md tells the model to use an MCP code index for code questions and to use grep only for exact text. The injected text says the opposite. Both are in context, and the model has no clear rule for which one wins. - It did happen. The model searched code with grep in an indexed repo, even though a written rule in the plan said to use the index. One of my sessions logged 930 Bash calls, and 362 of them were grep. - I cannot turn the text off. The only workaround is acceptEdits mode, but then shell commands prompt me and my autonomous builds stop. What I ask for (any one of these helps): 1. Remove the tool-choice paragraph from bypass mode. Bypass should only remove prompts. 2. Or remove "search with grep and find" from it. At minimum, limit it to exact text searches. 3. Or add one sentence: "User and project instructions (CLAUDE.md) and installed MCP tools take priority over this default." 4. Or add a setting in settings.json to turn the injected text off. Environment: Claude Code on Windows 11, bypassPermissions mode, several MCP plugins installed (including a code index).

Environment Info

• Platform: win32
• Terminal: vscode
• Version: 2.1.280
• Feedback ID: 3613d8d7-69e9-4ff9-96ae-28597683f75a

Errors

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