In the method JavaCompilerTool.getTask() 'options' can be supplied in the place of 'classes' and still JavaCompilerTool will work fine.
Please see the code:
<code>
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import javax.tools.*;

import static javax.tools.StandardJavaFileManager.StandardLocation.*;
import static javax.tools.JavaFileObject.Kind.*;

public class Foo1 {
     private void test(String... args) throws Throwable {
        JavaCompilerTool javac = ToolProvider.getSystemJavaCompilerTool();
        DiagnosticListener<? super javax.tools.JavaFileObject> dl =
                    new DiagnosticListener<javax.tools.JavaFileObject>() {
            public void report(Diagnostic message) {
                System.out.print("\nFile Name : "+new File(
                        message.getSource().toString()).getName());
                System.out.print("\nProblem Found : "+message.getKind());
                System.out.print("\nLine Number : "+message.getLineNumber());
                System.out.print("\nMessage : "+message.toString());
                System.out.println("\nCode : "+message.getCode());
            }
        };
        JavaFileManager jfm = javac.getStandardFileManager(null);
        JavaFileObject jfo = jfm.getJavaFileForInput(CLASS_PATH,args[0],SOURCE);
        StandardJavaFileManager sjfm = javac.getStandardFileManager(dl);
        Iterable<? extends JavaFileObject> iteJFO = sjfm.getJavaFileObjectsFromFiles(
                                               Arrays.asList(new File(args[0])));
        List<String> options = new ArrayList<String>();
        options.add("-Xlint");
        JavaCompilerTool.CompilationTask task =
                javac.getTask(null,sjfm,dl,null,options,iteJFO);
        task.run();
    }
    public static void main(String... arg) throws Throwable {
        try{
            List<Integer> list = new ArrayList();
            Foo1 test = new Foo1();
            test.test("Foo1.java");
        } catch(Exception ex) {
                ex.printStackTrace();
                System.exit(1);
        }
    }
}
</code>
In the above code I am passsing options in the place of classes, still it works fine instead of throwing exception.
<output>
bash-3.00$ java Foo1

File Name : Foo1.java
Problem Found : MANDATORY_WARNING
Line Number : 37
Message : Foo1.java:37: warning: [unchecked] unchecked conversion
found : java.util.ArrayList
required: java.util.List<java.lang.Integer>
Code : compiler.warn.prob.found.req
</output>
JavaCompilerTool successfully expanded -Xlint though it is given in the place of classes.

<java-version>
bash-3.00$ java -version
java version "1.6.0-beta2"
Java(TM) SE Runtime Environment (build 1.6.0-beta2-b82)
Java HotSpot(TM) Client VM (build 1.6.0-beta2-b82, mixed mode)
</java-version>