JIRA requires various directory paths to operate (search index path, attachment path, backup path). These are currently stored in the database. This is bad, because directories are specific to the server machine, not the data. Directory paths should be stored in the app server with all the other (non-portable) configuration data, rather than in the (portable) JIRA data.

For instance, it should be possible to set the JIRA index directory with a system property (-Djira.indexpath=/var/jira/indexes), or perhaps via a JNDI entry.