This fixes up the FlagBufferZones which was causing an out-of-bounds error, (and not doing the right thing). Issue is that we start the Index from 1, not the GridStartIndex. This was offsetting the flagging by 2 zones, and running off the edge.
Since I was at it, I also found how to clean up most if not all of the remaining valgrind warnings that occur between when the data is fully loaded and intialized and when it is written out. There are still pieces that have to do with MPI initialization and some read/writing of data that pop up.
Mesh Dimension was not ever initialized for < 3D datasets, led to "uninitialized variable warnings"
SiblingList[grid1].GridList can either be a single pointer or an array of pointers depending on "NumberOfGrids". This now matches the logic from CreateSiblingList.C and Grid_FastSiblingLocatorFindSiblings.C
I ran push suite against 7f39d6602fbc. Several tests throw errors. All of the differences relate to differences in output times, which in turn gives differences in field results. There has been a significant amount of work since then, it would be nice to understand the differences that have cropped up in the last 4 months. However none look like they're related to these changes, so I'll go ahead and approve this PR.