In most of the normal usage, we will be calling Standard java file manager as, JavaCompiler.StandardJavaFileManager(null,null,null).
How about providing one more method getStandardJavaFileManager() which internally calls getStandardJavaFileManager(null,null,null) like

StandardJavaFileManager getStandardFileManager() {
    getStandardFileManager(null,null,null);
}

Also same for Tool.run(), one more method can be added some thing like
int run(String... arguments) {
        run(null, null, null, arguments);
}