A DESCRIPTION OF THE PROBLEM :
Wen running javadoc with both a class in the unnamed package and also a package, all are included but the overview page does not have any link to the class in the unnamed package. While I haven't tested this with regressions, I believe it did work fine with JDK 8 (the last version that produced HTML frames by default).

Running javadoc on just classes in the unnamed package does work, but not if you include named packages on the command line too.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
C:\Users\wpollock\Temp\dir>javadoc -d docs Main.java foo
Loading source file Main.java...
Loading source files for package foo...
Constructing Javadoc information...
Standard Doclet version 15.0.1+9
... (No warnings or errors produced)

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
opening docs/index.html should show an overview of two packages, but only the named package shows. The other file was included, as can be confirmed by browsing the index.
ACTUAL -
opening docs/index.html only shows the one package.

---------- BEGIN SOURCE ----------
C:\Users\wpollock\Temp\dir>type Main.java
// Demo for javadoc issue
import foo.Bar;

/** Class in unnamed package to test javadoc version 15.
 */
public class Main {
    /** main method.
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        Bar b = new Bar();
    }
}

C:\Users\wpollock\Temp\dir>type foo\Bar.java
// Demo class for javadoc issue

package foo;

/** Bar is for yada. Yada-yada.
 */
public class Bar {}

---------- END SOURCE ----------

FREQUENCY : always