When updating the phpRunner build on the host, be sure to make a copy of the site BEFORE uploading the phpRunner build, then copy the following files and folders to the newly updated version. These will be overwritten by phpRunner when the build is uploaded.

DMS or DMSV10/
customStyles.css
scriptsAjax.js 
reportsAjax.php
scriptsJavascript.js
runReport.php

folders in DMS or DMSV10/
bs
tabPages
scripts
plugins - we decided to NOT copy this folder into DMSV10 from the DMSV10_OLD site since we don't know if the items in it are even being used or if they are old files that are no longer needed. If there are any issues we can copy these files from production into the test site.