- *.stx are (mostly arbitrary) reference structured text files, and

- *.ref are previously processed output from the corresponding *.stx files.

Here's the in-depth explanation:

The directory has a bunch of .stx files (ones found on the zope.org
site, plus an 'examples.stx' file, for accumulating a body of
examples) plus corresponding .ref files, previously produced by a
prior, established StructuredText version.  The script 'regress'
applies the new ../StructuredText.py version to produce .new files,
and then compares the .ref files and the .new files, complaining if
any differences are found.

The intended procedure is to make your changes in ../StructuredText.py,
iron them out as best you can, and then try the regress script to
identify any unexpected functionality changes/backwards-compatability
losses.  (We also need to develop the body of reference text and examples.)