Use the following regex commands in Vim or a plugin like Vintageous to clean up broken links in the footnote section. Select the text in the footnote section, hit :, and paste in the following commands:
# fix the links that are chopped in half by a tag
s:</span></a>([^<]*)</p>:\1</span></a></p>:g
# or, if there is a span around the content
s:</span></a><span class="e-link">([^<]*)</span></p>:\1</span></a></p>:g
# make the href match the url in the text
s:<a href="[^<]*"><span class="e-link">(http[s]?.//[^<]*)</span></a></p>:<a href="\1"><span class="e-link">\1</span></a></p>:g
For fixing . included in href problem:
# just .
s:(http[s]?.//[^<]*)\.</span></a></p>:\1</span></a>.</p>:g
s:(http[s]?.//[^<]*)\.("><span class="e-link">):\1\2:g
# . and space
s:(http[s]?.//[^<]*)\. </span></a></p>:\1</span></a>.</p>:g
s:(http[s]?.//[^<]*)\. ("><span class="e-link">):\1\2:g
- note, these could possibly be cleaned up. second set may not be necessary if problems from 1st set are resolved with a smarter regex
To create links
s:(https?.//[^\s<]*):<a href="\1"><span class="e-link">\1</span></a>:g
# isolate to just ones that are inside a bare p
s:(https?.//[^\s<]*)\s*</p>:<a href="\1"><span class="e-link">\1</span></a></p>:g
Add link onto a naked span
s:<span class="e-link">(https?.//[^\s<]*)</span>\s*</p>:<a href="\1"><span class="e-link">\1</span></a></p>:g
from scratch
add stuff
s:\n+\s*(.+):\n\n<div id="footnote-xxx" class="_idFootnote"><p class="e-footnote-text"><a class="_idFootnoteAnchor _idGenColorInherit" href="case-studies-2_New_Zealand_Christchurch_Earthquakes.html#footnote-xxx-backlink">x</a>\1</p></div>:g
add a div, probably not needed unless i screw up again
s:\n+\s*(.+):\n\n\1</div>:g
convert to something real
s:<div id="footnote-xxx" class="_idFootnote"><p class="e-footnote-text"><a class="_idFootnoteAnchor _idGenColorInherit" href="case-studies-2_New_Zealand_Christchurch_Earthquakes.html#footnote-xxx-backlink">x</a>([0-9][0-9]?):<div id="footnote-\1" class="_idFootnote"><p class="e-footnote-text"><a class="_idFootnoteAnchor _idGenColorInherit" href="case-studies-2_New_Zealand_Christchurch_Earthquakes.html#footnote-\1-backlink">\1</a>:g