Standard compilers use fixed -O3 pipelines that miss workload-specific speedups due to the Phase-Ordering Problem. Autotune Doctor is an AI-guided CLI that discovers, validates, and mathematically proves custom LLVM pipelines outperforming -O3. Unlike research tools, it tests on real silicon, enforces bitwise correctness gates, validates with Welch's t-test (p<0.05), and exports drop-in CMake recipes and CI guards. Install via PyPI: pip install autotune-doctor