clang Warnings with new JavaNativeAccessWrappers

@claus.kleinwort found these warnings on his MacBook while testing !2 (merged) . The full output is fairly long so I'll just list the items that jump out to me.

1. The defined macro has "undefined behavior". This warning accounts for most of the printouts - I'll need to research into this to see how to avoid it.
2. Comparison of std::size_t and int in a loop. This is because int can be negative and std::size_t can't be. Can avoid this by aligning types.
3. ptr_array_to_vector has C-linkage but uses a user-defined type. I think this can be avoided by moving that vector out of the extern "C" block.
4. points_2 and npoints_2 are unused parameters. This is definitely a typo on my part that got past my testing.
5. level is an unused parameter. Probably can remove if printTrajectory does not use the level parameter anymore.
6. unused variable out - probably can remove.

I can work on drafting patches to resolve these warnings, but since I don't have a MacBook I'll need help testing that these patches function as intended.