Let $d$ be a (well-behaved) shortest-path metric defined on a path-connected subset of $\mathbb{R}^2$ and let $\mathcal{D}=\{D_1,\ldots,D_n\}$ be a set of geodesic disks with respect to the metric $d$. We prove that $\mathcal{G}^{\times}(\mathcal{D})$, the intersection graph of the disks in $\mathcal{D}$, has a clique-based separator consisting of $O(n^{3/4+\varepsilon})$ cliques. This significantly extends the class of objects whose intersection graphs have small clique-based separators. Our clique-based separator yields an algorithm for $q$-COLORING that runs in time $2^{O(n^{3/4+\varepsilon})}$, assuming the boundaries of the disks $D_i$ can be computed in polynomial time. We also use our clique-based separator to obtain a simple, efficient, and almost exact distance oracle for intersection graphs of geodesic disks. Our distance oracle uses $O(n^{7/4+\varepsilon})$ storage and can report the hop distance between any two nodes in $\mathcal{G}^{\times}(\mathcal{D})$ in $O(n^{3/4+\varepsilon})$ time, up to an additive error of one. So far, distance oracles with an additive error of one that use subquadratic storage and sublinear query time were not known for such general graph classes.
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