Previously when entering a file to be run (console, workflow function, script field etc) you were required to give the full script path, or the path relative to the catalina.base directory.
When the plugin is first installed it will create a directory called "scripts" under your JIRA home directory, and register it as one of its script roots. This should be sufficient for most users and no other configuration need be made. This is a logical place to store your scripts, as it’s preserved during JIRA upgrades, and by definition will be accessible by all nodes in a clustered JIRA.
For instance, a script and a class:
<jira-home>/scripts/foo.groovy