Use relative module qualifiers for namespaces

[valeriabarra]

It is recommended that submodules refer to other modules within the enclosing parent module (including the latter) using relative module qualifiers in using and import statements.

For instance, in src/ConservationChecker.jl, we want to avoid

using ClimaCoupler.Utilities: CoupledSimulation

in favor of:

using ..Utilities: CoupledSimulation

The same pattern applies elsewhere too.

This issue is part of SDI #205