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refactor(1089): update index types from int to size_t #3084

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Job	Run time
build_cbind	3m 17s
CrossSection:ON false GCC 13	10m 10s
build_mac (OFF)	4m 23s
CrossSection:ON false GCC 14	9m 56s
build_mac (ON)	3m 45s
build_mac_builtin_tbb	4m 5s
CrossSection:ON true GCC 13	5m 14s
CrossSection:ON true GCC 14	5m 3s
build_mxe (OFF)	3m 22s
build_wasm (OFF)	6m 27s
CrossSection:OFF true GCC 14	4m 4s
build_mxe (ON)	5m 2s
build_windows (OFF)	7m 32s
build_wasm (ON)	4m 19s
build_windows (ON)	6m 1s
build_mac_builtin_tbb_subdir	1m 36s
build_nix (manifold-none)	4m 17s
build_nix (manifold-tbb)	3m 15s
build_nix (manifold-js)	25m 36s
build_nix (manifold-js-tbb)	22m 57s
build_nix (manifold3d)	1m 55s
	2h 22m 16s