Example errors in apache log:
[Fri Jan 15 10:22:48.830746 2016] [:error] [pid 7764] [client ::1:41462] PHP Notice: Undefined index: symlink in /var/www/html/knowledgeroot-1.0.4/include/class-tree.php on line 262, referer: http://localhost/knowledgeroot-1.0.4/index.php?id=23&eid=27
Fix after running the upgrade_mysql.sql from the dumps directory:
Run these in mysql or phpmysqladmin
ALTER TABLE `tree` ADD `symlink` int(11) NOT NULL default '0';
ALTER TABLE `tree` ADD `sorting` int(11) NOT NULL default '0';
ALTER TABLE `files` ADD `counter` int(11) NOT NULL default '0';
This will fix your file attachments and symlink log errors.
You can also install the ckeditor extention and literally copy the latest version of ckeditor over the older one, which was nice.