Default system keystore is in:
$JAVA_HOME/lib/security/jssecacerts
or in:
$JAVA_HOME/lib/security/cacerts

Custom keystore can be set either in /etc/sysconfig/gitbucket by
specifying the following option:
GITBUCKET_JVM_OPTS="-Djavax.net.ssl.trustStore=/path/to/your/cacerts"
or in Gitbucket's System Settings.