For some reason, my clearspace installation (1.4.0 as a tomcat webapp) is defaulting to HTML markup, not wiki markup. The rich text editor is writing HTML, not WIKI, and the document viewer is only display HTML correctly. Anything in wiki is being displayed raw, and not formatted.
This means all of our old documents have stopped displaying correctly.
I can think of nothing that would have changed to cause this.
What do I do to change it back to using wiki markup rather than HTML?
It sounds like your wiki syntax filter got changed. To change it back, in the admin console go to Spaces->Settings->Filters and macros. You'll find the wiki syntax filter under the section labeled filters.