Let’s Encrypt – Is Certbot Good for HTTPS Certificates?

TL;DR

For everything to work and not only your browser, you need to add that CA certificate to the system's trusted CA repository.

In ubuntu:

• Go to /usr/local/share/ca-certificates/
• Create a new folder, i.e. "sudo mkdir school"
• Copy the .crt file into the school folder
• Make sure the permissions are OK (755 for the folder, 644 for the file)
• Run "sudo update-ca-certificates"

Why

Let me explain what is going on also, so the other posters see why they don't need any certificate to use Github over HTTPS.

What is going on there is that your school is intercepting all the SSL communications, probably in order to monitor them.

To do that, what they do is in essence a "man in the middle" attack, and because of that, your browser complains rightfully that he is not being able to verify github's certificate. Your school proxy is taking out github's cert and instead providing its own cert.

When your browser tries to verify the school's provided cert against the CA that signed github's cert, it rightfully fails.

So, for the SSL connection to work in the school, you need to consciously accept that "MITM" attack. And you do that by adding the school's CA certificate as a trusted one.

When you trust that school CA, your verification of the fake github cert will work, since the fake github cert will be verified by the school CA.

Be aware that SSL connection is not safe anymore since your school administrator will be able to intercept all your encrypted connections.

I "fixed" the configuration by myself, with a bit of luck.

The issue seems to have been caused by the default configuration Ubuntu is shipping with Apache v2.x.

After enabling the needed modules with something like

sudo a2enmod ssl
sudo a2enmod headers
sudo a2enmod socache_shmcb

I also enabled the "default SSL site" with

sudo a2ensite default-ssl

Then added my own stuff in the /etc/apache2/sites-enabled directory.

I added something like:

01-mysite.conf
02-other.conf
03-thistoo.conf

After running certbot --apache the directory content became:

01-mysite-le-ssl.conf
01-mysite.conf
02-other-le-ssl.conf
02-other.conf
03-thistoo-le-ssl.conf
03-thistoo.conf

The problem came from the fact that the "default SSL site" configuration file is called default-ssl.conf while the "default plaintext site" configuration is called 000-default.conf .

In my specific case, then, default-ssl.conf was the last one to be read by Apache v2.x from the sites-enabled directory:

000-default.conf
01-mysite-le-ssl.conf
01-mysite.conf
02-other-le-ssl.conf
02-other.conf
03-thistoo-le-ssl.conf
03-thistoo.conf
default-ssl.conf

By "simply" renaming default-ssl.conf to 000-default-ssl.conf I started having things working, after a mandatory reload: systemctl apache2 reload; systemct apache2 status!

The very same nmap command seen in the question now returns the expected results:

$ nmap -A -Pn -p 443 mysite.com.
Nmap scan report for mysite.com. (1.2.3.4)
Host is up (0.044s latency).
Other addresses for mysite.com. (not scanned): 1234:1234:123:1234::
rDNS record for 1.2.3.4: host1.hosting.net

PORT    STATE SERVICE  VERSION
443/tcp open  ssl/http Apache httpd 2.4.41
| tls-alpn: 
|_  http/1.1
|_http-title: 421 Misdirected Request
|_http-server-header: Apache/2.4.41 (Ubuntu)
|_ssl-date: TLS randomness does not represent time
| ssl-cert: Subject: commonName=host1
| Subject Alternative Name: DNS:host1
| Not valid before: 2022-11-06T10:22:12
|_Not valid after:  2032-11-03T10:22:12
Service Info: Host: 127.0.0.1

Service detection performed. Please report any incorrect results at https://nmap.org/submit/ .
Nmap done: 1 IP address (1 host up) scanned in 15.74 seconds

It seems nmap doesn't know how to place a well-formed HTTPS SNI request.

But now we have: 443/tcp open ssl/http Apache httpd 2.4.41 : now it's ssl/http, not just http!

Lesson learned: with SSL/TLS and SNI, order matters. And a lot too!

As a very minor side note, I cleaned up the non-SSL (aka "HTTP") configuration file like this:

<VirtualHost _default_:80>
  ServerName  mysite.com # <-----------------.
  RewriteEngine on #                         | THE SAME
  RewriteCond %{SERVER_NAME} =mysite.com # <-'
  RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,NE,R=permanent]
</VirtualHost>

All other configuration stuff has been moved into the SSL-enabled configuration. Simple and effective!

I really hope this will help others.