Use a build tool such as Ant or Maven. Both lets you manage dependencies in a much better way than can be accomplished using e.g. the find UNIX tool. Both And and Maven also lets you define custom tasks to be performed in addition to compilation. Maven furthermore comes with conventions for managing external dependencies in remote repositories, as well as conventions for running unit tests and features that support continuous integration.
Even if you just need to compile your source files once in a while, you'll probably find that setting up a simple Ant build.xml file can be a big time saver in the end.
Finally, most of the popular IDE and code editor applications has some kind of integration with Ant build scripts, so you can run all the Ant tasks from within the editor. NetBeans, Eclipse, IDEA and more also has built-in support for Maven.
Read this first, if you're new to Ant. Below is the example build file from the link:
simple example build file
Once you're familiar with Ant, you'll find it easier to move to Maven.
