Editing java files can't use FTP?

Hi, A developer has built our site in java/javascript however I can't seem to figure out how to edit the files? Apparently it can't be done in FTP. Looking for someone to explain how I can do it myself. In the main directory it seems to be : [login to view URL] /war/ /tomcat/ /java/ /cgi-ban/ whats unimportant and whats important for the actual script? My thoughts is the script is some how in the .war file? Tomcat and Java are plugins/systems for the script to work. Help appreciated. Thanks.