Remove flow_funcs from the base namespace

This PR is for finishing up the details of the refactoring of the flow and connectivity packages. Following the discussion at #1162 , I've removed the functions that implement flow algorithms from the base namespace and also renamed files in the flow package so modules and functions have different names; we obey the informal module-name-must-be-unique rule. Updated tests and docstrings. The later need a bit more work to clearly explain that flow functions have to be explicitly imported from the flow package.

Also adapted the connectivity package to the changes in the flow package.