The FAQ for file permissions is a bit buried. I looked in this forums FAQ section, and then in the docs/FAQ file as distributed with the applications, and finally found it on the wiki at: https://pkp.sfu.ca/wiki/index.php/PKP_Frequently_Asked_Questions#I.27m_having_file_permission_problems.3B_how_should_I_set_file_permissions.3F
I’ve promoted this post to the forum’s FAQ:
The second link in the wiki FAQ was broken, but has been relinked.