Address comments from Chris

docs/doxygen/Doxyfile.in

@@ -757,6 +757,7 @@ INPUT                  = @CMAKE_SOURCE_DIR@/docs/doxygen/ \
                          @CMAKE_SOURCE_DIR@/library/LibUtilities/ \
                          @CMAKE_SOURCE_DIR@/library/StdRegions/ \
                          @CMAKE_SOURCE_DIR@/library/SpatialDomains/ \
+                         @CMAKE_SOURCE_DIR@/library/Collections/ \
                          @CMAKE_SOURCE_DIR@/library/LocalRegions/ \
                          @CMAKE_SOURCE_DIR@/library/MultiRegions/ \
                          @CMAKE_SOURCE_DIR@/library/GlobalMapping/ \

library/Collections/BwdTrans.cpp

@@ -1052,7 +1052,7 @@ class BwdTrans_SumFac_Pyr : public Operator
             int mode  = 0;
             int mode1 = 0;
             int cnt   = 0;
-            for (i = mode = mode1 = 0; i < m_nmodes0; ++i)
+            for (i = 0; i < m_nmodes0; ++i)
             {
                 for (j = 0; j < m_nmodes1; ++j, ++cnt)
                 {