In order to better maintain our Jira installation, we did a clean install and then checked in /var/atlassian and /opt/atlassian directory contents into a subversion repository. The idea being that any change made (to configration or plugins) will be easy to track, maintain and revert if needed. However I noticed that on restarting of Jira it keeps removing the jar files within /var/atlassian/application-data/jira/plugins/.bundled-plugins/ directory. I manually restored the contents twice just to be sure.
What am I missing here?
The $JIRA_HOME/plugins/.bundled-plugins is a directory where JIRA will automatically deploy the bundled plugin. The bundled plugins are the plugin listed under the Administrations > Manage Add-Ons > System > and thus you should not be worry about this directory ;) . Because it is auto-deploy when JIRA startup.
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