JavaCompilerTool can compile and generate '.class' of non '.java' files.
<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 Foo {
    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.println("\nFile Name : "+new File(
                        message.getSource().toString()).getName());
            }
        };
        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:all");
        JavaCompilerTool.CompilationTask task =
            javac.getTask(null,sjfm,null,options,null,iteJFO);
        task.run();
    }
    public static void main(String... arg) throws Throwable {
         Foo test = new Foo();
         test.test("Bar.other");
    }
}
</code>
<Bar.other>
class Bar {
}
</Bar.other>
After running the code, Bar.class file will be created.

When I run Bar.other in the command line, compiler will throw the following error:
error: Class names, 'Bar.other', are only accepted if annotation processing is explicitly requested
1 error

I feel it will be good, if JavaCompilerTool also throws the same exception.