Sphinx warnings: automodapi problems?

Looks a lot like https://github.com/astrofrog/wcsaxes/issues/79.  I don't understand how https://github.com/astrofrog/wcsaxes/pull/83 fixed it.  @cdeil, any tips, since you seem to be the sphinx guru?

```
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.contextmanager'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.convolve'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.convolve_fft'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.downsample_axis'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.flatten_header'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.get_cd'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.get_pixel_mapping'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.get_spectral_mapping'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.load_header'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.match_images.flatten_header'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.match_images.load_header'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.match_images.regrid_cube_hdu'
<autosummary>:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.header_tools.get_cd'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.contextmanager'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.convolve'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.convolve_fft'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.downsample_axis'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.flatten_header'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.get_cd'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.get_pixel_mapping'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.get_spectral_mapping'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.cube_regrid.load_header'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.match_images.flatten_header'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.match_images.load_header'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.match_images.regrid_cube_hdu'
None:None: WARNING: toctree contains reference to nonexisting document u'api/FITS_tools.header_tools.get_cd'
```