Fixing io docs links for  issue 1221

This PR fixes most of the broken links (~300) in the io modules for issue #1221. The remaining ones are mainly the ``'Bases'`` links, and other automodapi generated ones. 

For some reason the automodapi is not included in the astropy.io.fits docs, causing broken `astropy.io.fits` or :mod:`astropy.io.fits`, etc links. Should these links be removed or point to somewhere else?