We construct holonomic quantum gates for qubits that are encoded in the near-degenerate vibrational -doublet of a deformable three-body system. Using Kendall’s shape theory, we derive the Wilczek–Zee connection governing adiabatic transport within the -manifold. We show that its restricted holonomy group is , implying universal single-qubit control by closed loops in shape space. We provide explicit loops implementing a phase gate and a Hadamard-type gate. For two-qubit operations, we outline how linked holonomic cycles in arrays generate a controlled Chern–Simons phase, enabling an entangling controlled- (CNOT) gate. We present a Ramsey/echo interferometric protocol that measures the Wilson loop trace of the Wilczek–Zee connection for a control cycle, providing a gauge-invariant signature of the non-Abelian holonomy. As a physically realizable demonstrator, we propose bond-length modulations of a Cs()–Cs()–Cs() Rydberg trimer in optical tweezers and specify operating conditions that suppress leakage out of the -manifold.

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