This page contains related questions on Git Integration for JIRA add-on SSH connections in JIRA.
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Passphrases are now supported since v2.x.x of the Git Integration Plugin for JIRA add-on.
SSH keys should be in .ssh folder located in user home (user which is used to run jira). Note that JIRA 5 is using 'jira' user for run by default.
The PRIVATE KEY is needed by the SSH client, which is the JIRA server, to connect to the Git server via SSH.
Configure SSH remote git repositories with Connect to Git Repository wizard as you would with any remote git repository.
Here's a video to guide you step-by-step as stated above: