Used this quick Python script with manual whitespace
cleanup.

import sys
def link_de_dup(filename):
    links = []
    text = []
    for line in open(filename):
        if line.startswith(".. _"):
            links.append(line)
        else:
            text.append(line)
    with open(filename, "w") as handle:
        for line in text:
            handle.write(line)
        for line in sorted(set(links)):
            handle.write(line)
for filename in sys.argv[1:]:
    print("Processing %s" % filename)
    link_de_dup(filename)

Could be more clever about sorting the issue and pull request
links numerically rather than alphabetically...

Spotted using command line too rst-lint from
https://pypi.python.org/pypi/restructuredtext_lint

Fixes unused hyperlink target warning via rst-lint tool
from https://pypi.python.org/pypi/restructuredtext_lint

Fixes unused hyperlink target warning via rst-lint tool
from https://pypi.python.org/pypi/restructuredtext_lint
about ``Common Workfow Language`` by using this rather
than ``CWL``.

This allows us to remove the ``CWL`` link target, and thus
avoid that being a duplicate link in setup.py when the
``README.rst`` and ``HISTORY.rst`` files are combined. That
solves one of the complaints from ``make lint-readme``.

Fixes unused hyperlink target warning via rst-lint tool
from https://pypi.python.org/pypi/restructuredtext_lint
about  by using this rather than
.

This allows us to remove the  link target, and thus
avoid that being a duplicate link in setup.py when the
 and  files are combined. That
solves one of the complains from if [ -f .venv/bin/activate ]; then . .venv/bin/activate; fi; python setup.py check -r -s
running check.

Spotted using rst-lint README.rst from
https://pypi.python.org/pypi/restructuredtext_lint

Spotted via https://pypi.python.org/pypi/restructuredtext_lint
since rst-lint README.rst gives much more helpful messages than
make lint-readme