Apache NetBeans 20: Apache Tomcat service doesn't stop when I try to stop it from the IDE

Question

The issue is this one: I've configured in the IDE both the "Catalina Home" and "Catalina Base" directories to setup the Apache Tomcat Server on NetBeans 20.

I've previously set my "/etc/tomcat9/tomcat-users.xml" like this:

<?xml version="1.0" encoding="UTF-8"?>
<!--
  Licensed to the Apache Software Foundation (ASF) under one or more
  contributor license agreements.  See the NOTICE file distributed with
  this work for additional information regarding copyright ownership.
  The ASF licenses this file to You under the Apache License, Version 2.0
  (the "License"); you may not use this file except in compliance with
  the License.  You may obtain a copy of the License at

      http://www.apache.org/licenses/LICENSE-2.0

  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
-->
<tomcat-users xmlns="http://tomcat.apache.org/xml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.0" xsi:schemaLocation="http://tomcat.apache.org/xml tomcat-users.xsd">
    <!--
  By default, no user is included in the "manager-gui" role required
  to operate the "/manager/html" web application.  If you wish to use this app,
  you must define such a user - the username and password are arbitrary.

  Built-in Tomcat manager roles:
    - manager-gui    - allows access to the HTML GUI and the status pages
    - manager-script - allows access to the HTTP API and the status pages
    - manager-jmx    - allows access to the JMX proxy and the status pages
    - manager-status - allows access to the status pages only

  The users below are wrapped in a comment and are therefore ignored. If you
  wish to configure one or more of these users for use with the manager web
  application, do not forget to remove the <!.. ..> that surrounds them. You
  will also need to set the passwords to something appropriate.
-->
    <!--
  <user username="admin" password="<must-be-changed>" roles="manager-gui"/>
  <user username="robot" password="<must-be-changed>" roles="manager-script"/>
-->
    <!--
  The sample user and role entries below are intended for use with the
  examples web application. They are wrapped in a comment and thus are ignored
  when reading this file. If you wish to configure these users for use with the
  examples web application, do not forget to remove the <!.. ..> that surrounds
  them. You will also need to set the passwords to something appropriate.
-->
    <!--
  <role rolename="tomcat"/>
  <role rolename="role1"/>
  <user username="tomcat" password="<must-be-changed>" roles="tomcat"/>
  <user username="both" password="<must-be-changed>" roles="tomcat,role1"/>
  <user username="role1" password="<must-be-changed>" roles="role1"/>
-->
    <!-- user manager can access only manager section -->
    <role rolename="manager-gui"/>
    <!-- user admin can access manager and admin section both -->
    <role rolename="admin-gui"/>
    <user password="root" roles="manager-gui,manager-script,admin" username="root"/>
    <user password="root" roles="manager-gui,admin-gui,manager-script,admin" username="root"/>
</tomcat-users>

Since I was having a permission trouble, because the IDE wasn't able to write the logs and other stuff on the proper directory, I solved that by doing:sudo chmod 777 -R /var/lib/tomcat9

I could then properly connect to the database by doing:

Connection con = DriverManager.getConnection(urlRoot + dbName, "root", "root");

Being the whole URL: jdbc:mysql://localhost:3306/mercado

Despite the application worked fine, it doesn't stop the Tomcat server when I click the "Stop" (Red square) at the IDE, so I had to manually kill the process by using "htop". So on, that process deleted me some folders at "/var/log", and broke both my "apache2" and "mongodb" services, so I had to reinstall them to make them work properly again.

The screenshots of my Apache Tomcat config are these ones:

And the libraries configuration in my project is this one:

I can't reproduce again the faliure, since it may break my Apache and MongoDB installations again, or even more things.

Any idea of what can be going wrong? If there's any more information needed, please tell me.