wagon-plugins are for deploying artifacts to repositories, repositories need all those other files to function. If you are trying to ftp your .war file to a server for deployment, then use the correct plugin for your server, not the wagon-plugin.
The documentation for that plug starts off with
In order to deploy artifacts using FTP ...
mvn deploy
is for deploying artifacts to a repository, thus all the other files that are needed for the repository to function are uploaded as well.