NOISSUE rearrange build system

* Added install commands to the libraries instead of force installing files
* Most of the application cmake stuff moved to top level
* RPATH should now be set/cleared correctly
* Contains a fix for GH-1780

libraries/javacheck/CMakeLists.txt

@@ -11,3 +11,4 @@ set(SRC
 )
 
 add_jar(JavaCheck ${SRC})
+install_jar(JavaCheck "${JARS_DEST_DIR}")