Allow duplication of GeoAlignableTransforms for alignable elements

Replaces !396 (closed)

Change to try and address Issue #116. The same GeoAlignableTransform was being used for multiple elements to be aligned because the de-duplication already found a transformation with that name, so it returned that instead of creating a new one.

FYI @tsulaia @jojungge @rbianchi

GeoModelTools/GeoModelXML/GeoModelXml/GeoModelXml/Element2GeoItem.h

@@ -32,7 +32,7 @@ class Element2GeoItem: public GeoDeDuplicator {
 public:
     Element2GeoItem() = default;
     virtual ~Element2GeoItem() = default;
-    GeoIntrusivePtr<RCBase> process(const xercesc::DOMElement *element, GmxUtil &gmxUtil);
+    GeoIntrusivePtr<RCBase> process(const xercesc::DOMElement *element, GmxUtil &gmxUtil, const bool &allowDuplication=false);
     virtual GeoIntrusivePtr<RCBase> make(const xercesc::DOMElement *element, GmxUtil &gmxUtil) const;
 protected:
     using EntryMap = std::map<std::string, GeoIntrusivePtr<RCBase>>;