Change Deck access methods/types to references

opm-parser#677 changes the return types for the Deck family of classes.
This patch fixes all broken code from that patch set.

https://github.com/OPM/opm-parser/pull/677

examples/sim_poly_fi2p_comp_ad.cpp

@@ -155,7 +155,7 @@ try
     std::shared_ptr<EclipseState> eclipseState;
     try {
         deck = parser->parseFile(deck_filename , parseMode);
-        Opm::checkDeck(deck);
+        Opm::checkDeck(deck, parser);
         eclipseState.reset(new Opm::EclipseState(deck , parseMode));
     }
     catch (const std::invalid_argument& e) {