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How I can create dedicated FTP user for Java application?

Main FTP user (the same as cPanel user) has access to all files and directories in home directory including Tomcat directory tree with webapps. You can use this account to update your web applications.

If you want to delegate access to a single web application to a separate user then create new FTP user in cPanel - Files - FTP Accounts.

Set its directory path to the path to your web application. For example if you have MyWebApp application in Tomcat webapps directory
the 'Directory' path will look similar to
/home/username/appservers/apache-tomcat-7.0.28/webapps/MyWebApp

The part printed in red is what you append to the fixed prefix part (your home directory).

This directory will become root and home directory for the new FTP user. He will not be able to browse anything else above this directory. Files uploaded and modified by the new FTP user will continue to be owned by your main FTP user.

This hint applies as well to other Java application servers hosted by us.