I finally decided to follow recommended security guidelines and move the system file above web root on an MSM deployment. It worked fine for the main site, and I could access the control panels of all MSM sites, but the MSM sites kept giving me the error:
Your system folder path does not appear to be set correctly. Please open the following file and correct this: index.php
I experimented by adding and subtracted dots to no avail. No matter what I’ve done, I keep getting the same error message from my MSM secondary sites. My secondary sites are in subfolders under the public_html directory. Everything seems to work fine as long as the system file remains in that directory.
I’m running EE 2.5.1 on EngineHosting.