Fix whitespace in topic, university, workflow docs

Many code blocks are 4spaced, and they render in GitLab
without coloring as a result, even though they are
fenced with a language label. If in a list, other items
will render as being in a code block too, even if not
meant to. This fixes all these issues, and cleans up
minor white space issues in /topic, /university, /update
and /workflow docs.