Checkpointing reference implementation updates

* Add _print_error() helper function for printing exceptions to sys.stderr.  These are not hidden
  behind -v
* `warnings` can be lazy imported.
* Since the site.toml file is no longer proposed, rewrite how .pth and .start files are parsed and
  processed.
* addpackage() -- which was never documented -- is deprecated; there are a few usages in the wild so
  we can't get rid of it, but it's generally unnecessary now, has different semantics.
* Update tests

Author: warsaw