Cleanup particleIndex, uint64_t and ints all over the library

The type usage for storing particle count, particle indices is inconsistent across the library, most of the particle count queries are returning integers, while the particle index is defined as uint64_t. Internally it's stored using ints.

Simply get rid of the custom definitions and rely on size_t, which is always the biggest size type on any platform. No need for any custom types.
