more work on documentation

doc/conf/conf.py

modules/base/doc/generic.rst

modules/conop/doc/conop.rst

modules/doc/newmodule.rst

modules/geom/doc/geom.rst

modules/img/alg/doc/alg.rst

modules/img/base/doc/img.rst

modules/index.rst

modules/io/doc/io.rst

modules/io/pymod/__init__.py

modules/mol/base/doc/editors.rst

modules/mol/base/doc/entity.rst

modules/mol/base/doc/mol.rst

modules/seq/base/doc/seq.rst