You can get the current home directory of a Jenkins server at "Manage Jenkins -> Configure System -> Home Directory".
When starting a Jenkins server, you can specify its home directory through setting environment variable JENKINS_HOME:
export JENKINS_HOME=~/.jenkins
then
java -jar <jenkins-ver.war> --httpPort=8088
or start as a daemon service:
nohup java -jar <jenkins-ver.war> --httpPort=8088 1>jenkins.log 2>jenkins.log &
When update Jenkins or install some new plugins, you may find all jobs gone. Don't be panic, it's probably because the home folder are changed (for example, ~/.hudson) by the plugins. Specify home directory as above, all jobs will come back.