Is a gravitational singularity distinct from a topological hole?

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In the context of a spacetime (e.g., definition 1 here) of classical general relativity theory, what is the technical mathematical difference(s) between a gravitational singularity and a topological hole? The two seem similar, naively, in the sense that neither are considered to be "part" of the manifold, and that one cannot continuously shrink the manifold beyond it.

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If you take a geodesically complete manifold and remove a disk (make a hole) where at least one geodesic passes through, then you get a manifold with a hole which is geodesically incomplete and you have that sort of spacetime singularity.

On the other hand, a singularity of spacetime is not necessarily a hole. For instance, consider the maximal extension of Schwarzschild spacetime, which is homeomorphic to a contractible region in $R^4$. The region $r=0$ where the singularity lies is not topologically a hole but a spacelike hypersurface $T^2-X^2=1$. Here $T$ and $X$ are the Kruskal-Szekeres coordinates.