Main.java

package pg;

@interface Keep {
}

public class Main {
  public static void main(String[] args) throws Exception {
    System.out.println(
        Class.forName(System.getenv("THE_CLASS"))
            .getMethods()[0].invoke(null));
  }
}

@Keep
class Helper {
  @Keep public static String getString() {
    return "success!";
  }
}

Makefile

go:
	$(RM) -r bin out.jar
	mkdir bin
	$(JAVAC) -d bin Main.java
	$(JAVA) -jar $(PROGUARD_JAR) -verbose -include proguard.cfg
	$(JAVA) -classpath bin pg.Main
	$(JAVA) -classpath out.jar pg.Main

proguard.cfg

-dontpreverify
-dontoptimize
-injars bin
-outjars out.jar
-libraryjars  <java.home>/lib/rt.jar

-keepattributes *Annotation*

-keep class pg.Main {
  public static void main(java.lang.String[]);
}

# Uncommenting this makes the program work.
#-keep class pg.Keep

-keep @pg.Keep class *
-keepclassmembers class * {
  @pg.Keep *;
}

transcript.txt

$ make JAVAC=javac JAVA=java PROGUARD_JAR=/home/dreiss/stuff/build/proguard4.9beta2/lib/proguard.jar THE_CLASS="pg.Helper"
rm -f -r bin out.jar
mkdir bin
javac -d bin Main.java
java -jar /home/dreiss/stuff/build/proguard4.9beta2/lib/proguard.jar -verbose -include proguard.cfg
ProGuard, version 4.9 beta2
Reading input...
Reading program directory [/home/dreiss/work/proguard-test/bin]
Reading library jar [/home/dreiss/opt/jdk1.6.0_35/jre/lib/rt.jar]
Initializing...
Ignoring unused library classes...
  Original number of library classes: 17459
  Final number of library classes:    48
Shrinking...
Removing unused program classes and class elements...
  Original number of program classes: 3
  Final number of program classes:    2
Obfuscating...
Writing output...
Preparing output jar [/home/dreiss/work/proguard-test/out.jar]
  Copying resources from program directory [/home/dreiss/work/proguard-test/bin]
java -classpath bin pg.Main
success!
java -classpath out.jar pg.Main
Exception in thread "main" java.lang.ClassNotFoundException: pg.Helper
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:169)
	at pg.Main.main(Unknown Source)
make: *** [go] Error 1
$