The combination of configuration interaction and many-body perturbation theory methods (CI+MBPT) is extended to non-perturbatively include configurations with electron holes below the designated Fermi level, allowing us to treat systems where holes play an important role. For example, the method can treat valence-hole systems like Ir$^{17+}$, particle-hole excitations in noble gases, and difficult transitions such as the $6s rightarrow 5d^{-1}6s^2$ optical clock transition in Hg$^+$. We take the latter system as our test case for the method and obtain very good accuracy (~1%) for the low-lying transition energies. The $alpha$-dependence of these transitions is calculated and used to reinterpret the existing best laboratory limits on the time-dependence of the fine-structure constant.
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