Remove most uses of `order='F'` or `np.asfortranarray`.

[wkearn]

libtopotoolbox functions should generally be agnostic to the memory layout of their arguments, so it should be fine to pass row-major arrays to libtopotoolbox, as long as the dimensions are passed in the correct order (#200). We should not convert arrays to column-major order unless it is absolutely necessary. It is important, however, to ensure that the memory layout of all the arrays passed to a libtopotoolbox function is the same.

This depends on #199 and #200.