Make templates consistent with how links are checked- v2

This is a replacement for #65 - it splits the commit to only include changes to .md and .html files.

The old branch is preserved for posterity- we will be discarding the affected functions in tools/check anyway, so there is no need to merge that file to the main repo. If you'd like to try that modified version of the validator, it will remain on the old branch until this pull request is closed.
Interesting: reverting the changes to `reference.md` restores the span tags. Seems like the build process (tools/filters/id4glossary.py) specifically looks for the page subtitle to be "Reference".

I've reverted the reference.md changes, and changed the link text in index.md instead.

However, this has implications for template creators: their page will not build correctly if the document subtitle is changed. Should we change the build process, or the validator?