Make internal implementations "protected"

There is a lot of stuff in the package that is not supposed to be used by end users. However, it bubbles up in many places: IDE autocompletions, HTML docs search results, etc. I propose to systematically rename "internal" and "implementation" modules and classes by prefixing them with an underscore, e.g. lsdb._dask, lsdb._nested, etc. I also to propose to hide "public" stuff which is reimported in the top __init__.py.

Also see #767 for API HTML docs improvements.