How do you change the CLASSPATH within Java?

Update Q4 2017: as commented below by vda8888, in Java 9, the System java.lang.ClassLoader is no longer a java.net.URLClassLoader.

See “Java 9 Migration Guide: The Seven Most Common Challenges“

The class loading strategy that I just described is implemented in a new type and in Java 9 the application class loader is of that type.
That means it is not a URLClassLoader anymore, so the occasional (URLClassLoader) getClass().getClassLoader() or (URLClassLoader) ClassLoader.getSystemClassLoader() sequences will no longer execute.

java.lang.ModuleLayer would be an alternative approach used in order to influence the modulepath (instead of the classpath). See for instance “Java 9 modules – JPMS basics“.

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For Java 8 or below:

Some general comments:

you cannot (in a portable way that’s guaranteed to work, see below) change the system classpath. Instead, you need to define a new ClassLoader.

ClassLoaders work in a hierarchical manner… so any class that makes a static reference to class X needs to be loaded in the same ClassLoader as X, or in a child ClassLoader. You can NOT use any custom ClassLoader to make code loaded by the system ClassLoader link properly, if it wouldn’t have done so before. So you need to arrange for your main application code to be run in the custom ClassLoader in addition to the extra code that you locate.
(That being said, cracked-all mentions in the comments this example of extending the URLClassLoader)

And you might consider not writing your own ClassLoader, but just use URLClassLoader instead. Create a URLClassLoader with a url that are not in the parent classloaders url’s.

URL[] url={new URL("file://foo")};
URLClassLoader loader = new URLClassLoader(url);

A more complete solution would be:

ClassLoader currentThreadClassLoader
 = Thread.currentThread().getContextClassLoader();

// Add the conf dir to the classpath
// Chain the current thread classloader
URLClassLoader urlClassLoader
 = new URLClassLoader(new URL[]{new File("mtFile").toURL()},
                      currentThreadClassLoader);

// Replace the thread classloader - assumes
// you have permissions to do so
Thread.currentThread().setContextClassLoader(urlClassLoader);

If you assume the JVMs system classloader is a URLClassLoader (which may not be true for all JVMs), you can use reflection as well to actually modify the system classpath… (but that’s a hack;)):

public void addURL(URL url) throws Exception {
  URLClassLoader classLoader
         = (URLClassLoader) ClassLoader.getSystemClassLoader();
  Class clazz= URLClassLoader.class;

  // Use reflection
  Method method= clazz.getDeclaredMethod("addURL", new Class[] { URL.class });
  method.setAccessible(true);
  method.invoke(classLoader, new Object[] { url });
}

addURL(new File("conf").toURL());

// This should work now!
Thread.currentThread().getContextClassLoader().getResourceAsStream("context.xml");