Maybe
you should take a look at
Maven. Maven can handle multiple source paths, resource paths and dependencies for you.
You can set maven up so that it will build your application as a JAR, containing a main class and having all its runtime dependencies on the class path automatically. Building then becomes as easy as running the command "
mvn package".
Maven's norm is to have all your sources in
src/main/java/ and all your resources in
src/main/resources/. Dependencies should almost never be in the extension folder of your runtime, but you don't have to worry about this as Maven handles it for you automatically.