I’m using a theme which uses a lot of absolute references,
using href="{{ .Site.BaseURL }}{{ .RelPermalink }}" or href="{{ .Site.BaseURL }}{{ .URL }}".
These links get broken with complex BaseURL like in my example above :
It seems as you mention that href="{{ .RelPermalink }}" is enough, if I don’t define any base element in the head-section of the page.
This means that all links in the page, and thus in the content.md file, should be relative to the root of baseURL ( http://example.org/ ) and not relative to BaseURL itself, or to the root of the hugo directory.
If I want to define a link in a content.md file, I can use the relref shortcode to define a relative link to another .md file: