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fix(affected): unify 'affected tests' and dead-code queries between CLI and MCP (CLI stem bug) #568

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@ajianaz

Bug. CLI affected (main.rs:1325-1328) derives the stem with rsplit('/') then rsplit('.'), which returns the extension (rs), so the naming-convention strategy never matches. It also lacks LIKE escaping, runs N queries, and uses 8 patterns vs MCP's 6. #564 hardened only the MCP copy (tools.rs:585-740). Dead-code also diverges: CLI loads entry_point_patterns, MCP hardcodes vec![] (main.rs:1622-1672 vs tools.rs:1131-1180).

Direction. One query module for affected tests and dead code; CLI and MCP only format output. Add end-to-end tests with in-memory SQLite.

From the 2026-10 architecture review (deepening candidates, develop @ 147dd75).

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