Model ignored an explicit instruction to investigate through an MCP code graph and read source via shell instead

What happened
The user asked for an investigation of six indexed repositories through a GitNexus MCP server. The model made two graph queries per repository, then read the source with about forty-four Bash cat/sed calls across ten batches. The project's CLAUDE.md also said "Graph first; text search only for empty/UNKNOWN/literals" and "Never substitute grep for graph analysis".

Expected
The graph tools (query, context with include_content, cypher, trace, cluster resources) for the whole investigation.

What the user said
"Use gitnexus mcp and investigate how 6 harnesses I indexed are working with their agents." Mid-turn: "stop the shell reads, go back to the graph, and use clusters, tool_map, context with content, trace and cypher per harness before any file is opened by hand."

Repro
Configure an MCP code-intelligence server, instruct "use the MCP to investigate these repos", observe the model fall back to shell file reads after the first graph calls.

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