o Modify scale and reflect signature in FBiGeom, now it conforms to

iGeom. also this is related to MeshKit commit -
1274870693875c7566a1db64210
o Remove old trac pages
o Fix FBiGeom test cases.

doc/UG/moabUG.h

@@ -1179,7 +1179,7 @@ Initial results have demonstrated that the data abstraction provided by MOAB is
 
 [3]	T.J. Tautges, MOAB Meta-Data Information, 2010.
 
-[4]	T.J. Tautges, “MOAB - ITAPS – Trac.”, http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB
+[4]	T.J. Tautges, “MOAB - ITAPS – SIGMA.”, http://sigma.mcs.anl.gov/
 
 [5]	“MOAB Developers Email List.”, moab-dev@mcs.anl.gov.
 
@@ -1213,7 +1213,7 @@ Initial results have demonstrated that the data abstraction provided by MOAB is
 
 [20]	M. O. Deville, P. F. Fischer, and E. H. Mund, High-order methods for incompressible fluid flow. Cambridge, UK; New York: Cambridge University Press, 2002.
 
-[21]	T. J. Tautges, “MOAB Wiki.” [Online]. Available: http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. [Accessed: 30-Oct-2012].
+[21]	T. J. Tautges, “MOAB Wiki.” [Online]. Available: http://sigma.mcs.anl.gov/moab-library [Accessed: 20-Oct-2016].
 
 [22]	T. J. Tautges, “Canonical numbering systems for finite-element codes,” International Journal for Numerical Methods in Biomedical Engineering, vol. 26, no. 12, pp. 1559–1572, 2010.
 

itaps/fbigeom/FBiGeom.h

@@ -2686,7 +2686,7 @@ extern "C" {
      *
      * Reflect an entity across the given plane
      * \param instance FBiGeom instance handle
-     * \param geom_entity the entity to reflect
+     * \param geom_entity the entity to reflect, x, y, z coordinate of the point that the reflecting plane goes though
      * \param plane_normal_x x coordinate of the plane's normal
      * \param plane_normal_y y coordinate of the plane's normal
      * \param plane_normal_z z coordinate of the plane's normal
@@ -2694,16 +2694,14 @@ extern "C" {
      */
   void FBiGeom_reflectEnt( FBiGeom_Instance instance,
                          iBase_EntityHandle geom_entity,
-                         double plane_normal_x,
-                         double plane_normal_y,
-                         double plane_normal_z,
-                         int* err );
+                           double x, double y, double z, double norm_x, double norm_y,
+                           double norm_z,int* err );
 
    /**\brief  Scale an entity in the x, y, and z directions
      *
      * Scale an entity in the x, y, and z directions.
      * \param instance FBiGeom instance handle
-     * \param geom_entity the entity to scale
+     * \param geom_entity the entity to scale, x, y, z coordinate of the point that the scale plane goes though
      * \param scale_x factor to scale by in the x direction
      * \param scale_y factor to scale by in the y direction
      * \param scale_z factor to scale by in the z direction
@@ -2711,10 +2709,8 @@ extern "C" {
      */
   void FBiGeom_scaleEnt( FBiGeom_Instance instance,
                        iBase_EntityHandle geom_entity,
-                       double scale_x,
-                       double scale_y,
-                       double scale_z,
-                       int* err );
+                       double x, double y, double z, double x_factor,
+                       double y_factor, double z_factor, int* err );
 
     /**\brief  Geometrically unite entities
      *

itaps/fbigeom/FBiGeom_MOAB.cpp

@@ -1271,13 +1271,14 @@ void FBiGeom_rotateEnt(FBiGeom_Instance instance, iBase_EntityHandle ,
 }
 
 void FBiGeom_reflectEnt(FBiGeom_Instance instance, iBase_EntityHandle ,
-                        double , double , double ,
-                        int* err) {
+                        double, double, double, double,
+                        double, double, int* err) {
   RETURN(iBase_NOT_SUPPORTED);
 }
 
 void FBiGeom_scaleEnt(FBiGeom_Instance instance, iBase_EntityHandle ,
-                      double , double , double , int* err) {
+                      double,  double, double, double,
+                      double, double, int* err) {
   RETURN(iBase_NOT_SUPPORTED);
 }
 

itaps/fbigeom/testSmooth.cc

@@ -1291,7 +1291,7 @@ bool transforms_test(FBiGeom_Instance geom) {
    }
 
    // now reflect through y plane; should recover original bb
-   FBiGeom_reflectEnt(geom, brick, 0.0, 1.0, 0.0, &err);
+   FBiGeom_reflectEnt(geom, brick, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, &err);
    CHECK( "Problems reflecting brick for transforms test." );
 
    FBiGeom_getEntBoundBox(geom, brick, bb_min, bb_min + 1, bb_min + 2, bb_max,

itaps/fbigeom/testSmooth2.cc

@@ -1321,7 +1321,7 @@ bool transforms_test(FBiGeom_Instance geom) {
    }
 
    // now reflect through y plane; should recover original bb
-   FBiGeom_reflectEnt(geom, brick, 0.0, 1.0, 0.0, &err);
+   FBiGeom_reflectEnt(geom, brick, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, &err);
    CHECK( "Problems reflecting brick for transforms test." );
 
    FBiGeom_getEntBoundBox(geom, brick, bb_min, bb_min + 1, bb_min + 2, bb_max,

itaps/fbigeom/testgeom.cc

@@ -1164,7 +1164,7 @@ bool transforms_test(FBiGeom_Instance geom)
   }
   
     // now reflect through y plane; should recover original bb
-  FBiGeom_reflectEnt( geom, brick, 0.0, 1.0, 0.0, &err );
+  FBiGeom_reflectEnt( geom, brick, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, &err );
   CHECK( "Problems reflecting brick for transforms test." );
   
   FBiGeom_getEntBoundBox( geom, brick, bb_min, bb_min+1, bb_min+2, bb_max, bb_max+1, bb_max+2, &err );

src/io/WriteDamsel.cpp

 /* WriteDamsel.cpp
- * The Damsel library provides mesh-aware parallel I/O; see http://trac.mcs.anl.gov/projects/damsel/wiki for details,
+ * The Damsel library provides mesh-aware parallel I/O; see http://cucis.ece.northwestern.edu/projects/DAMSEL/ for details,
  * though for now that site is restricted to project participants.  Damsel uses a data model that's very similar to
  * that used in MOAB and ITAPS.  It uses the same basic data model concepts of entities, sets, tags, and interface.
  * In theory, we should be able to completely save/restore to/from Damsel any data that can be saved/restored to/from