Auto-mode instruction to prefer Bash cat/sed over dedicated tools conflicts with user and project instructions to use an MCP code graph

**What happened**
The session carried the system instruction "While auto mode is active: Do your work through the Bash tool wherever it can accomplish the job: read files with cat, head, or sed -n ... rather than using the dedicated Read, Edit, or Write tools." The user's instruction and the project CLAUDE.md required a graph-first workflow through an MCP server. The model's reads went through Bash.

**Expected**
User and project instructions to outrank the auto-mode nudge, or the nudge to state that it does not apply when an MCP tool is the requested path.

**What the user said**
"you were given utterly explicit instructions that had no clauses for you to violate and you chose to violate it"

**Repro**
Enable auto mode with an MCP code-intelligence server configured, instruct "use the MCP to investigate", observe tool choice.

**Environment:** Claude Code CLI 2.1.270 (Claude Code), macOS, auto mode, model claude-fable-5-1, session of 2026-09-14.