ISPConfig GitLab webfolder Empty after renewal Letsencrypt

Question

I have adopted a system where the certificate for the subdomain had to be renewed. There are two diffrent domains at the System, as an example.

• MainProject.de (The Website)[web1]
• sub.MainProject.de (GitLab)[web5]

The machine is a root system with Ubunutu 16.04.4(xenial). The Webserver is a Nginx 1.12.2

I have renewed the certificate with certbot and redirected the symlinks for the subdomain, because the certificate contains booth domains.

Then I realized that the web folder from the sub project was empty. There was the default start page.

the web folder /var/www/clients/client0/web5/web looks like

• error
• favicon.ico
• index.html
• robots.txt
• stats

I can not find the code from the subproject(GitLab) and thing that it was deleted. Before my renewal of the certificates the domain sub.MainProject.de works but without the SSL. Now it had SSL but shows the default empty page with the text "Welcome to your website!".

I have found at the Location (/var/opt/gitlab/git-data) the GitLab repositories, but there is no index.html where i can link the root directory in the Nginx config.

Here is my simplified history from the command.

vim /etc/letsencrypt/renewal/sub.MainProject.de.conf
vim /var/log/letsencrypt/letsencrypt.log
vim /etc/letsencrypt/live/sub.MainProject.de/
/etc/init.d/nginx restart
lsb_release -a
sudo apt-get update
sudo certbot renew --dry-run
sudo apt-get install software-properties-common
cd /etc/nginx/
sudo add-apt-repository ppa:certbot/certbot
sudo certbot --nginx
sudo apt-get update
sudo apt-get install python-certbot-nginx
sudo certbot --nginx certonly
service nginx restart
cd /var/www/sub.MainProject.de/ssl/
sudo ln -sf /etc/letsencrypt/live/MainProject.de/chain.pem sub.MainProject.de-le.bundle
sudo ln -sf /etc/letsencrypt/live/MainProject.de/fullchain.pem sub.MainProject.de-le.crt
sudo ln -sf /etc/letsencrypt/live/MainProject.de/privkey.pem sub.MainProject.de-le.key
service nginx restart
vim /etc/nginx/sites-available/sub.MainProject.de.vhost
cd /var/www/clients/client0/web5/
cd web/
ls -l
cd /etc/nginx/sites-available/
vim sub.MainProject.de.vhost
service nginx restart
cd /var/www/clients/client0/web5/
vim index.html
cd /var/opt/gitlab/git-data/repositories/MainProject/
cd /etc/gitlab/
vim gitlab.rb
sudo gitlab-ctl restart nginx
sudo gitlab-ctl restart status
sudo gitlab-ctl reconfigure
service nginx restart
sudo gitlab-ctl start
service nginx restart
sudo gitlab-ctl status

My vhost file from /etc/nginx/sites-available/sub.MainProject.de.vhost

server {

listen *:80;

listen *:443 ssl;
ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
ssl_certificate /var/www/clients/client0/web5/ssl/sub.MainProject.de-le.crt;
ssl_certificate_key /var/www/clients/client0/web5/ssl/sub.MainProject.de-le.key;

server_name sub.MainProject.de ;

root   /var/www/sub.MainProject.de/web/;

if ($scheme != "https") {
    rewrite ^ https://$http_host$request_uri? permanent;
}


index index.html index.htm index.php index.cgi index.pl index.xhtml;


location ~ \.shtml$ {
    ssi on;
}


error_page 400 /error/400.html;
error_page 401 /error/401.html;
error_page 403 /error/403.html;
error_page 404 /error/404.html;
error_page 405 /error/405.html;
error_page 500 /error/500.html;
error_page 502 /error/502.html;
error_page 503 /error/503.html;
recursive_error_pages on;
location = /error/400.html {
    internal;
}
location = /error/401.html {
    internal;
}
location = /error/403.html {
    internal;
}
location = /error/404.html {

    internal;
}
location = /error/405.html {

    internal;
}
location = /error/500.html {

    internal;
}
location = /error/502.html {

    internal;
}
location = /error/503.html {

    internal;
}

error_log /var/log/ispconfig/httpd/sub.MainProject.de/error.log;
access_log /var/log/ispconfig/httpd/sub.MainProject.de/access.log combined;

location ~ /\. {
    deny all;
}

location ^~ /.well-known/acme-challenge/ {
    access_log off;
    log_not_found off;
    root /usr/local/ispconfig/interface/acme/;
    autoindex off;
    index index.html;
    try_files $uri $uri/ =404;
}

location = /favicon.ico {
    log_not_found off;
    access_log off;
    expires max;
    add_header Cache-Control "public, must-revalidate, proxy-revalidate";
}

location = /robots.txt {
    allow all;
    log_not_found off;
    access_log off;
}

location /stats/ {

    index index.html index.php;
    auth_basic "Members Only";
    auth_basic_user_file /var/www/clients/client0/web5/web//stats/.htpasswd_stats;
}

location ^~ /awstats-icon {
    alias /usr/share/awstats/icon;
}

location ~ \.php$ {
    try_files /ee974d31eec46bbdc066e78824e61f10.htm @php;
}

location @php {
    try_files $uri =404;
    include /etc/nginx/fastcgi_params;
    fastcgi_pass unix:/var/lib/php7.0-fpm/web5.sock;
    fastcgi_index index.php;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
    fastcgi_intercept_errors on;
}

location /cgi-bin/ {
    try_files $uri =404;
    include /etc/nginx/fastcgi_params;
    root /var/www/clients/client0/web5;
    gzip off;
    fastcgi_pass  unix:/var/run/fcgiwrap.socket;
    fastcgi_index index.cgi;
    fastcgi_param SCRIPT_FILENAME  $document_root$fastcgi_script_name;
    fastcgi_intercept_errors on;
}

Thanks for the Help!