Imports in some `__init__.py` files should be made explicit

_Originally posted by @brgcode in https://github.com/compas-dev/compas/pull/1111#discussion_r1081776686_

The `__all__` attribute in some `__init__.py` files should be populated with items explicitly rather than with iteration on `dir()`.

For example here: https://github.com/compas-dev/compas/blob/b03002c9e55237405d1f4f8119edff13b42afc20/src/compas/geometry/primitives/__init__.py#L20