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refactor(1089): update index types from int to size_t #3055

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Job	Run time
build_mac (OFF)	4m 16s
CrossSection:ON false GCC 13	4m 40s
build_mac (ON)	3m 49s
build_cbind	2m 47s
CrossSection:ON false GCC 14	4m 40s
build_mac_builtin_tbb	2m 48s
CrossSection:ON true GCC 13	4m 40s
build_mac_builtin_tbb_subdir	1m 40s
build_mxe (OFF)	3m 24s
CrossSection:ON true GCC 14	4m 41s
build_mxe (ON)	4m 27s
CrossSection:OFF true GCC 14	4m 6s
build_nix (manifold-none)	1m 26s
build_wasm (OFF)	4m 38s
build_nix (manifold-tbb)	1m 57s
build_nix (manifold-js)	4m 40s
build_windows (OFF)	2m 49s
build_wasm (ON)	4m 4s
build_nix (manifold-js-tbb)	4m 41s
build_windows (ON)	2m 54s
build_nix (manifold3d)	2m 4s
	1h 15m 11s