What do we need to change to sign java appbundle since updating from 10.9.4 to 10.9.5

[Paul Taylor]

Can somebody help me with this please I just updated from OSX 10.9.4 to 
10.9.5, and it  looks like I have to change how I sign Java application 
after updating because Im now getting this output after signing with

     export 
CODESIGN_ALLOCATE="/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/codesign_allocate"
     /usr/bin/codesign --sign "Developer ID Application: P Taylor" 
--force --deep --verbose /Applications/SongKong.app

Im getting:

     /Applications/SongKong.app: the main executable or Info.plist must 
be a regular file (no symlinks, etc.)
     In subcomponent: 
/Applications/SongKong.app/Contents/PlugIns/jdk1.8.0_20.jdk

and verification with

     /usr/bin/codesign --verify --deep  --verbose /Applications/SongKong.app

gives me

     /Applications/SongKong.app: code object is not signed at all
     In architecture: x86_64

What do I have to change to fix this ?

Paul