I had been storing my modules, themes, etc outside of the document root, and using symlinks inside the document root. This runs afoul of checkPath() when trying to update from the UI, however. So I gave up and put the physical directories back inside the docroot.
And now the site doesn't work, because the system table has the old physical locations stored in it. Nothing seems to reset or rebuild those values. I would typically use the Registry Rebuild contributed Drush command in Drupal 7 to fix this kind of thing, but it hasn't been ported (yet).
Anyone know of anything that rebuilds system from the filesystem?