It appears that copy() is overprotective of open_basedir restrictions.

At the web host I administer we restrict each VirtualHost to the owning user's homedir using php_admin_value open_basedir /tmp:/home/user

All is well unless the user attempts to copy files. With ANY file copying operation, even copying files within one directory that is allowed by open_basedir, copy() fails with an open_basedir error (File is in wrong directory, open_basedir restriction in effect.) The directory the error complains about is ALWAYS allowed in the user's open_basedir setting.

This is especially evident when uploading files. open_basedir is set to allow for access to /tmp, but if users attempt to copy() an uploaded file from /tmp to /home/user, it gives an error. If the user instead calls move_uploaded_file() it is successful.