To add/remove/change virtual hosts, look into the following files:

/etc/lighttpd/vhosts.d/*.conf

The settings specified in them are included at /etc/lighttpd/lighttpd.conf by

include_shell "cat /etc/lighttpd/vhosts.d/*.conf"

(don't forget newlines at the end of .conf files being "catted").
After any modification of these files (or, generally, conf-files related to lighttpd)
you must verify the syntax by

>lighttpd -t -f /etc/lighttpd/lighttpd.conf

If "Syntax OK" message appears, run

>sudo service lighttpd restart

Since /etc/lighttpd is owned by root, sudo is required to edit these files.
Hint: run "sudo mc"...

To restart MySQL server, run

>sudo service mysql restart

not just "sudo mysqld" etc.

To install needed packages, run
>sudo apt-get install <package-name>

Don't remove "certbot" dir, it contains a script required to renew
SSL certificates from Let's Encrypt for websites being hosted (see /etc/letsencrypt as root).
This script, in "renew" mode, runs from "renew-ssl-certificates" (cron should execute it daily).