We present a multi-agent, human-in-the-loop workflow that co-designs quantum codes with prescribed transversal diagonal gates. It builds on the Subset-Sum Linear Programming (SSLP) framework (arXiv:2504.20847), which partitions basis strings by modular residues and enforces $Z$-marginal Knill-Laflamme (KL) equalities via small LPs. The workflow is powered by GPT-5 and implemented within TeXRA (https://texra.ai)-a multi-agent research assistant platform that supports an iterative tool-use loop agent and a derivation-then-edit workflow reasoning agent. We work in a LaTeX-Python environment where agents reason, edit documents, execute code, and synchronize their work to Git/Overleaf. Within this workspace, three roles collaborate: a Synthesis Agent formulates the problem; a Search Agent sweeps/screens candidates and exactifies numerics into rationals; and an Audit Agent independently checks all KL equalities and the induced logical action. As a first step we focus on distance $d=2$ with nondegenerate residues. For code dimension $K\in\{2,3,4\}$ and $n\le6$ qubits, systematic sweeps yield certificate-backed tables cataloging attainable cyclic logical groups-all realized by new codes-e.g., for $K=3$ we obtain order $16$ at $n=6$. From verified instances, Synthesis Agent abstracts recurring structures into closed-form families and proves they satisfy the KL equalities for all parameters. It further demonstrates that SSLP accommodates residue degeneracy by exhibiting a new $((6,4,2))$ code implementing the transversal controlled-phase $diag(1,1,1,i)$. Overall, the workflow recasts diagonal-transversal feasibility as an analytical pipeline executed at scale, combining systematic enumeration with exact analytical reconstruction. It yields reproducible code constructions, supports targeted extensions to larger $K$ and higher distances, and leads toward data-driven classification.

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