fixes compilation of xmodel_update when configured with ADIOS
removes obsolete links in README file
adds error checking when reading of Par_file parameters; updates user output in model_tomography.f90
renames output from xmeshfem3D to output_meshfem3D.txt (to avoid overwriting by xgenerate_databases); updates error messages
Merge branch 'devel' of https://github.com/geodynamics/specfem3d into devel