Adds replaceCore function that takes a matchVect (#1013)

* Adds replaceCore function that takes a matchVect

* Fixes error reporting, adds tests

* Switches PRECONDITION to ValueError exceptions

* Fixes MatchVectType annoyance in swig.  Don't know why this is necessary.

* Silences warnings

* Adds working doctests and better explanations.

Code/JavaWrappers/ChemTransforms.i

@@ -33,6 +33,8 @@
 
 %{
 #include <GraphMol/ChemTransforms/ChemTransforms.h>
+// Fixes annoying compilation namespace issue
+typedef RDKit::MatchVectType MatchVectType;
 %}
 
 %newobject deleteSubstructs;