I've been wrestling with this for a week now, and I now admit I'm not going to solve this without some help.
Situation: I have a licensed copy of Confluence 6.9.1. Setting it up for vanilla http was simple. I then generated a self-signed certificate and stepped through the how-tos and was able to get everything working fairly quickly using the self-signed cert.
The next logical step was getting a verified certificate, which I did through GoDaddy. The Tomcat collection of certs contains the actual certificate for my FQDN, a gd_bundle-g2-g1.crt and a gdig2.crt.pem intermediate cert.
I have fought with keytool and openssl in vain to get a workable cert configuration for my setup. I've executed how-to documents found on a dozen other websites, the instructions provided by GoDaddy, stuff on the Confluence website--and still, what I get when I attempt to use some varietal of the certs provided by GoDaddy, I get a dead site.
If there is someone out there who has successfully installed GoDaddy SSL certificates for Confluence, I would be grateful for a simple step-by-step "HOW I DID IT" a la Young Frankenstein.