Quote from: gibbs_ at Dec 10, 2011, 12:30 AMAre there any other directories that should stay accessible? Currently only the manager and connectors directory are and I am getting some odd behaviour with packages. I imagine that might be related to the core (will test).
All of the files and folders except the core have to remain web accessible (when installing the advanced package you get the option to locate and customize the paths for the main web directory, as well as the manager and connectors folders). If you install the advanced package after relocating the core outside the webroot, setup will allow you to configure the core location as the first step when it can't find it in the standard location and will configure the appropriate custom core location throughout the MODX installation.
To resolve any issues with paths, especially regarding packages, just re-run setup as an upgrade.