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The challenge of quantum computing is to combine error resilience with universal computation. Diagonal gates such as the transversal $T$ gate play an important role in implementing a universal set of quantum operations. This paper introduces a framework that describes the process of preparing a code state, applying a diagonal physical gate, measuring a code syndrome, and applying a Pauli correction that may depend on the measured syndrome (the average logical channel induced by an arbitrary diagonal gate). It focuses on CSS codes, and describes the interaction of code states and physical gates in terms of generator coefficients determined by the induced logical operator. The interaction of code states and diagonal gates depends very strongly on the signs of $Z$-stabilizers in the CSS code, and the proposed generator coefficient framework explicitly includes this degree of freedom. The paper derives necessary and sufficient conditions for an arbitrary diagonal gate to preserve the code space of a stabilizer code, and provides an explicit expression of the induced logical operator. When the diagonal gate is a quadratic form diagonal gate (introduced by Rengaswamy et al.), the conditions can be expressed in terms of divisibility of weights in the two classical codes that determine the CSS code. These codes find application in magic state distillation and elsewhere. When all the signs are positive, the paper characterizes all possible CSS codes, invariant under transversal $Z$-rotation through $\pi/2^l$, that are constructed from classical Reed-Muller codes by deriving the necessary and sufficient constraints on $l$. The generator coefficient framework extends to arbitrary stabilizer codes but there is nothing to be gained by considering the more general class of non-degenerate stabilizer codes.

The teleportation model of quantum computation introduced by Gottesman and Chuang (1999) motivated the development of the Clifford hierarchy. Despite its intrinsic value for quantum computing, the widespread use of magic state distillation, which is closely related to this model, emphasizes the importance of comprehending the hierarchy. There is currently a limited understanding of the structure of this hierarchy, apart from the case of diagonal unitaries (Cui et al., 2017; Rengaswamy et al. 2019). We explore the structure of the second and third levels of the hierarchy, the first level being the ubiquitous Pauli group, via the Weyl (i.e., Pauli) expansion of unitaries at these levels. In particular, we characterize the support of the standard Clifford operations on the Pauli group. Since conjugation of a Pauli by a third level unitary produces traceless Hermitian Cliffords, we characterize their Pauli support as well. Semi-Clifford unitaries are known to have ancilla savings in the teleportation model, and we explore their Pauli support via symplectic transvections. Finally, we show that, up to multiplication by a Clifford, every third level unitary commutes with at least one Pauli matrix. This can be used inductively to show that, up to a multiplication by a Clifford, every third level unitary is supported on a maximal commutative subgroup of the Pauli group. Additionally, it can be easily seen that the latter implies the generalized semi-Clifford conjecture, proven by Beigi and Shor (2010). We discuss potential applications in quantum error correction and the design of flag gadgets.