Is the configuration option http.sslcainfo supposed to be working in EGit/JGit? It doesn't seem to be working for me with .pem files in EGit 126.96.36.199305112223. Command-line Git (188.8.131.52) is happy with these files.
If it's not implemented yet, is it in the queue of pending tasks?
Currently http.sslcainfo is not supported by JGit. I have some ooold proposals ,  which add client and server side support for certificate based authentication to JGit. They'll bring http.sslcainfo. Somehow I had not enough time to finish this and forgot about them. From my perspective the demand for this feature was also not so high. But I think it's time not to get this through. I'll continue to work on these two changes and propose some updated commits.
The main utility of http.sslcainfo is for servers that for whatever reason need to use self-signed certs for https access. In this case remote operations like clone, push and fetch won't work without this feature, unless you disable verification altogether (http.sslVerify=false), which is vulnerable to man-in-the-middle attacks.