Use relative links in `doc`, fix broken generated HTML links

Links like (doc/web_hooks/web_hooks.md) work in the GitLab source code web interface, but the HTML generator produces broken links in the doc subdirectories:
http://doc.gitlab.com/ce/hooks/doc/web_hooks/web_hooks.html
instead of the right one
http://doc.gitlab.com/ce/web_hooks/web_hooks.html
in
http://doc.gitlab.com/ce/hooks/custom_hooks.html.

Fixes #14338 (closed)