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Let d be a (well-behaved) shortest-path metric defined on a path-connected subset of ℝ² and let 𝒟 = {D_1,…,D_n} be a set of geodesic disks with respect to the metric d. We prove that 𝒢^×(𝒟), the intersection graph of the disks in 𝒟, has a clique-based separator consisting of O(n^{3/4+ε}) 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+ε}), 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+ε}) storage and can report the hop distance between any two nodes in 𝒢^×(𝒟) in O(n^{3/4+ε}) 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.