The JavaScript "link fix" looks to be only needed for pages
where Markdown is included, and which contain relative links.
Now that we modified all local includes to use absolute links,
the only location where links are not properly generated, is
in the reference documentation.
If broken links are found elsewhere in the website, those links
are legitimately broken, and should be fixed in the markdown
source, not fixed-up afterwards.
This patch moves the javascript to the cli.md include, so that
the script is only run on the reference pages instead of on every
page.
Signed-off-by: Sebastiaan van Stijn <github@gone.nl>