I wanted to comment on this bug, which I am also experiencing. I apologize for writing to the developer list, but the bug tracker signup said that "due to spam" I would have to do it this way...
I am running Jenkins in a terminal window in Ubuntu 15.10 via "java -jar jenkins.war" and configuring it in a browser window.
I set up two credentials as "SSH username with private key". One of them is generated without a passphrase and the other with. When I configure my build to use the one with the passphrase, a prompt of this form appears in the terminal window in which Jenkins is running:
Enter passphrase for key '/tmp/ssh4822078610521010444key':
If I enter the passphrase here the build proceeds. When I use the credential that has *no* passphrase, but is otherwise generated identically, no password prompt appears and the build works without manual intervention.
Expected result: Jenkins uses the passphrase stored in the configured credential instead of prompting.
I am running Jenkins 1.645, Git plugin 2.4.1 and Git client 1.19.1. I hope this information is useful.
Best Regards,
Jeff