Solve deform matrix directly

This commit goes back to the original direct solution of deform matrix
instead of using optimization.
Clean codes

Remove DeformMatrixFitting codes from Tracer.
Add timer in AdvectionManager::connectTracersAndMesh.
Supplement full lat-lon initial distribution of tracers in TracerManager.
Add adjusting codes for skeleton points so that the body coordinates of
them can be changed.
Adapt to the changes in GeoMTK