Eliminate the "store" global variable

Also, move a few free-standing functions into StoreAPI and Derivation.

Also, introduce a non-nullable smart pointer, ref<T>, which is just a
wrapper around std::shared_ptr ensuring that the pointer is never
null. (For reference-counted values, this is better than passing a
"T&", because the latter doesn't maintain the refcount. Usually, the
caller will have a shared_ptr keeping the value alive, but that's not
always the case, e.g., when passing a reference to a std::thread via
std::bind.)

src/nix-store/xmlgraph.cc

@@ -33,7 +33,7 @@ static string makeNode(const string & id)
 }
 
 
-void printXmlGraph(const PathSet & roots)
+void printXmlGraph(StoreAPI & store, const PathSet & roots)
 {
     PathSet workList(roots);
     PathSet doneSet;
@@ -51,7 +51,7 @@ void printXmlGraph(const PathSet & roots)
         cout << makeNode(path);
 
         PathSet references;
-        store->queryReferences(path, references);
+        store.queryReferences(path, references);
 
         for (PathSet::iterator i = references.begin();
              i != references.end(); ++i)