Why? "[NOT IN USE ANYMORE, PLEASE USE SSL Cert Manager and AutoSSL]"

Really?

CWP don't have support for the Let's Encrypt?

I think that is one of the top features...

I want to know this too
best feature is let's encrypt

They still support the LE SSL but location is changed. You can find this in the SSL Cert Manager option from left side.

http://i66.tinypic.com/291zspz.jpg

AUTO SSL IS Let's Encrypt.

What I want to know is why they keep the menu.

With this change, how does one add a cert for sub domains, like I used for my control panel?

simply select user and then select subdomain from dropdown

We have the option to ANY domain on that menu, but NOT to the main domain, the hostname domain.
(as 'hostname domain' I'm regarding the process to get the certificate from LetsEncrypt)

This was definitely disabled...??!!

There are videos on youtube, but this option simply don't work anymore like that.

Ok, I've tried the following:
http://wiki.centos-webpanel.com/hostname-ssl-with-letsencrypt

but that page is not updated.

Seems the correct menu has changed:
Instead:
In cwp.admin left menu go to –> CWP Settings –> Change Hostname save there your hostname...

read:
In cwp.admin left menu go to –> Server Settings –> Change Hostname save there your hostname.

There are some problem with the pointing of the certificate.
I spend three days working on this.

The program creates correctly the certificates at '/etc/pki/tls/certs/', but the certificate directive in the file '/usr/local/cwpsrv/conf/cwpsrv.conf' with:
-----------------------------------------------------------
ssl_certificate     /etc/pki/tls/certs/hostname.crt;
-----------------------------------------------------------

when my server is working only with:
-----------------------------------------------------------
ssl_certificate     /etc/pki/tls/certs/hostname.bundle;
-----------------------------------------------------------

It's a bug..??!!