When you start the forge server jar for the first time using java 6 without using the command line, i.e. by double clicking on it, forge puts the server files, server.properties, mods folder, etc., in the home folder on linux. However, if you start the forge server jar using the command line or using a .sh start file, the server files are put into the directory the forge server jar is in. The files being put in the home folder can become a bit of a hassle if the computer is being used for storing different servers files.

 

I don't know if this is intentional, and if it wasn't I just wanted to point it out.

Thanks

It puts the files into the current working directory. So however you have java assigned to run is where things go. Typically it's the directory that has the file.