Hello Robert,
There is a trick here: your ssl certificate must be trusted by both your JVM and by the native "git" executable.
The native "git" executable picks its certificates from "/etc/ssl/certs/" on ubuntu, the folder should be similar on other linux distributions.
The default JVM SSL trust store is $JAVA_HOME/jre/lib/security/cacerts and, on OS like ubuntu, is a symlink to /etc/ssl/certs/java/cacerts
I like to use "jrunscript" to test the trust store of java virtual machines. If the invocation returns an http code, then the certificate is trusted by the JVM:
jrunscript -e "println(new java.net.URL(\"https://github.acme\").openConnection().getResponseCode())"
Cyrille