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.