whitespace cleanup in docs

doc/src/Section_commands.txt

doc/src/Section_howto.txt

doc/src/Section_packages.txt

doc/src/Section_python.txt

doc/src/accelerate_intel.txt

doc/src/bond_oxdna.txt

doc/src/compute_cnp_atom.txt

doc/src/dump_vtk.txt

doc/src/fix_box_relax.txt

doc/src/fix_eos_table_rx.txt

doc/src/fix_filter_corotate.txt

doc/src/fix_gcmc.txt

doc/src/fix_grem.txt

doc/src/fix_ipi.txt

doc/src/fix_mscg.txt

doc/src/fix_nve_dot.txt

doc/src/fix_nve_dotc_langevin.txt

doc/src/fix_nvk.txt

doc/src/fix_spring.txt

doc/src/neb.txt