It seems I now have to use the --deep
option
I also figured out that I can just refer to ceritificate by name
e.g.
export CODESIGN_ALLOCATE="/Applications/Xcode.app/Contents/Developer
/Toolchains/XcodeDefault.xctoolchain/usr/bin/codesign_allocate"
/usr/bin/codesign --deep --force --sign "Developer ID Application: P Taylor" /Applications/Jaikoz.app
/usr/bin/codesign --deep -v /Applications/Jaikoz.app