I wanted to post an update in case anyone else runs into this problem because I think I have found a solution.
I ran "sudo ln -s /etc/mysql/my.cnf /etc/my.cnf" because I think it was looking for /etc/my.cnf instead of /etc/mysql/my.cnf. This seems to have fixed that problem. When I ran mysql -u root again I got a new error "ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: NO)". I fixed that by running "mysql --user=root -p" and entering a new password.
I think I have mysql set up correctly. I am going to work on sourcing my database. However, the guide says that the databasefile.sql should be in server/database but I don't have the database directory. I'm going to try and find it. Does my eqemu_config.xml look correct from a couple posts back?
Thank you.
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