I have been codesigning my Runtime for some years now. The Terminal codesigning worked well up to and including OS X 10.10.5.
Under OS X 10.11.1, the codesigning is rejected ("obsolete resource envelope") and GateKeep will not open my Runtime. I searched the internet and came across this site describing a similar error, diagnosis, and probable cause: http://furbo.org/2015/07/23/code-signing-in-el-capitan/
When I checked my runtime, I found this:
codesign --verbose=4 --deep --strict MyRuntime.app
MyRuntime.app: invalid destination for symbolic link in bundle
In subcomponent: /Users/MyUser/Desktop/MyRuntime.app/Contents/Frameworks/DBEngine.framework
file modified: /Users/MyUser/Desktop/MyRuntime.app/Contents/Frameworks/DBEngine.framework/Versions/Current/A
The other Frameworks in the bundle validated correctly.