How can I delete the world file in a minecraft server

First stop your server, then go to your server files and delete the folder with the name "world" and then put whatever plugin you want in the plugins folder and then restart the server. It should work in that way, and also when you start the server, the server will automatically generate a world. I don't know much about plugins, but if your plugin uses a world gen system (something like mutiworld) then it will need a world to start with. A server cannot be started without a world create and you will not be able to use the in game plugin commands without the server started.

I hope this helped, if not then sorry.