RFR: JDK-8188768 Fix interaction between make and autoconf after consolidation

[Magnus Ihse Bursie]

Since the forest consolidation, multiple "paper-cut" issues have appeared.

This patch will deal with the following issues:
* Changes in autoconf files will no longer cause make to require a 
reconfigure.
* "make reconfigure" was broken when closed sources were present
* The new relationship between open and closed code allows for a more 
streamlined support for custom extensions in the open code.

Bug: https://bugs.openjdk.java.net/browse/JDK-8188768
WebRev: 
http://cr.openjdk.java.net/~ihse/JDK-8188768-fix-make-and-autoconf-interaction/webrev.01

/Magnus