Is a nucleus a collection of quarks or a collection of neutrons and protons? I do not much about particle physics. But people say that neutron and proton are composed of quarks, and in turn a nucleus is composed of neutrons and protons. 
Therefore, the question is, is this hierarchy necessarily well defined? Could we view a nucleus as a collection of quarks, without the in-between neutrons or protons? 
 A: 
Could we view a nucleus as a collection of quarks, without the in-between neutrons or protons? 

Conceptually this is similar to asking "could we view a building as a collection of bricks cement glass and iron". In some sense, one can, but it would be a funny way of defining a building because there is a hierarchy, and just the materials do not a building make.
A proton and neutron are a collection of quarks organized by the strong  force, in a whole, with small leaks of the strong force, called nuclear force, which allow for neutrons and protons to organize into nuclei.
The strong force is studied with lattice QCD which has fitted the observed spectra of bound quarks.
The nuclei are studied with the shell model using the nuclear force, which fits the observed periodic table of elements.
So it is all due to the self organization that the forces impose on  complex systems composed of quarks. 
One can say that people are a collection of quarks and electrons after all, as far as elementary particles are involved, ignoring the organizing principles of the forces between them.
