Tidy std::unique_ptr<>&& usage as an argument and just use std::unique_ptr<>

[SingingTree]

Code such as

void SetAtoms(std::unique_ptr<AtomHolder>&& atom_holder);

could be

void SetAtoms(std::unique_ptr<AtomHolder> atom_holder);

without changing much code wise or functionality wise. This complies better with Google style (though I kinda prefer the former).

[SingingTree]

This can be done for other rvalue usage too, as appropriate.