As you might already think, I'm a noob and I'm really desperate. I had this ibdata1 file with over 13 GB. I read that if I'd add innodb_file_per_table to the [mysqld] section of my.cnf, data wouldn't be stored anymore in ibdata1 and I could delete this file, which I did. I restarted everything and nothing was anymore like before. Neither me via phpmyadmin nor other services could connect to my database. I removed innodb_file_per_table from my.cnf and restarted mysql, which failed :(
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