Hardcoded URL for internal links

[knabar]

In a number of places, internal links are using https://www.openmicroscopy.com/ instead of {{ site.baseurl }}.

[knabar]

There are hardcoded site URLs in more places than I initially expected: master...knabar:www.openmicroscopy.org:fix-base-url

@jburel Is this something we want to fix wholesale, or individually as time goes on?

[jburel]

I think we might have to do some bundles at the time to check if the formatting is correct and make sure the links work
For the links we could run linkcheck, for the formatting it will have to be manual

But if you have done a lot of the work, I am happy to review it