Update deprecated boost/filesystem/convenience.hpp includes

modules/gui/src/python_shell/python_interpreter.cc

modules/io/src/mol/dcd_io.cc

modules/io/src/mol/entity_io_crd_handler.cc

modules/io/src/mol/entity_io_mae_handler.cc

modules/io/src/mol/entity_io_mmcif_handler.cc

modules/io/src/mol/entity_io_pdb_handler.cc

modules/io/src/mol/entity_io_pqr_handler.cc

modules/io/src/mol/pdb_reader.cc

modules/io/src/mol/pdb_writer.cc

modules/io/src/mol/sdf_reader.cc

modules/io/src/mol/sdf_writer.hh

modules/io/src/mol/surface_io_msms_handler.cc

modules/io/src/seq/clustal_io_handler.cc

modules/io/src/seq/fasta_io_handler.cc

modules/io/src/seq/hhm_io_handler.cc

modules/io/src/seq/pir_io_handler.cc

modules/io/src/seq/promod_io_handler.cc

modules/io/src/seq/pssm_io_handler.cc

modules/mol/alg/src/entity_to_density.cc

modules/mol/alg/src/lddt.cc