while I did not do this for apple development code signing, I still think I have some valuable inside that could help you debug such a problem. The difference is that I created my own certificate while you got one from apple.
Check the trust of the cert, it must be trusted for code signing (on yosemite that is the third last in the trust section of the cert view in the keychain access). Be aware that for your code signing the cert should be in the login keychain, I needed it in the System keychain.
At first the cert was not known for codesigning to the keychain, because there was the Extension purpose "Code Signing" missing, you can find this if you look into the keychain and double click on the certificate:
I fixed that (you can not fix it as Apple provides the cert to you. The extension should just be there):
Then I added the certificate to the trusted signing certificates, after I had drag&dropped the certificate from the keychain to my desktop, which created the ~/Desktop/gdb-cert.cer (be aware you can omit -d and -r trustRoot:
$ sudo security add-trusted-cert -d -r trustRoot -p codeSign -k /Library/Keychains/System.keychain ~/Desktop/gdb-cert.cer
This was a bit tricky because I was mislead by some internet posts and did not look at the man page. Some said you should use add-trust (https://llvm.org/svn/llvm-project/lldb/trunk/docs/code-signing.txt). The terrible bit was that the command succeeded, but did not do what it should.
After that I found the new cert in the trusted certs like so:
$ security find-identity -p codesigning
Policy: Code Signing
Matching identities
1) E7419032D4..... "Mac Developer: FirstName LastName (K2Q869SWUE)" (CSSMERR_TP_CERT_EXPIRED)
2) ACD43B6... "gdb-cert"
2 identities found
Valid identities only
1) ACD43... "gdb-cert"
1 valid identities found
In my case the apple cert is expired, but the one I was using to sign gdb was not (well, I just created it myself). Also be aware that the policy is named differently for the "security add-trusted-cert"(-p codeSign) and the "security find-identity" command (-p codesigning). I then went on to sign gdb and I also always got:
$ codesign --sign gdb-cert.cer --keychain ~/Library/Keychains/login.keychain `which gdb`
gdb-cert.cer: no identity found
because I was under the impression that I had to give the file name of the cert file to the --sign option, but that in fact was the CN of the certificate that I should have provided and should be in the trust store. You can find the CN here when double clicking on the cert in the keychain:
or in the above output of "security find-identity -p codesigning". Then I went on to sign and I had to give it the right keychain. In your case this would have to be the ~/Library/Keychains/login.keychain, in my case the System.keychain:
codesign -s gdb-cert --keychain /Library/Keychains/System.keychain `which gdb`
That then gave me a working gdb and it should give you a signed application.