Structure Files
$JIRA_HOME/structure
Structure keeps most of its data in the structure
sub-directory under the JIRA home directory.
Database
Structure uses embedded Apache Derby database engine to store its data in structure/db
directory.
Undo Logs for Synchronizers
When synchronizers change issues in background - either when running Export or Resync or when running incremental synchronization - they store the undo information in special log files in structure/syncundo
directory. The log files are kept for some time (~ 30 days b default) and then removed.
In case an incorrectly configured synchronizer ruins issue data (for example, Links synchronizer is able to remove all links of specific type when told to do so), the logs from syncundo sub-directory may be used to recover the data.
Backing up Structure Files
When JIRA is not running or when Structure plugin is disabled, you can manually back up structure directory (separately or as a part of JIRA home backup). Likewise, you can manually restore the structure
subdirectory if Structure plugin is not running - but be careful when downgrading to previous version of the Structure. As a rule, the database is not forward-compatible, so you can't downgrade and keep the database unless the versions of the Structure happen to have the same database schema.
You can also back up Structure into XML by using Structure Backup menu on the administrator's page.