RFR [9] 8134779 & 8134847: Minor usability issues with the jmod tool

[Chris Hegarty]

This is a minor change for a couple of usability issues with the jmod tool.
It now issues a warning when it encounters duplicate entries, or an out
of place module-info.class.

http://cr.openjdk.java.net/~chegar/8134779_8134847/

https://bugs.openjdk.java.net/browse/JDK-8134779
https://bugs.openjdk.java.net/browse/JDK-8134847

-Chris.