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Download Jython 2.5.0 from http://jython.org/downloads.html and install it: java -jar jython_installer-2.5.0.jar. Please do not use other versions (even later ones), this is known to cause bugs.
Set Java property for JIRA: -Dpython.home=<jython install directory> (follow this guide)
Download JSS 1.1 Plugin JAR (jss-1.1.jar), Initial scripts package (jss_base_scripts.zip) and On-edit Validator & Postfunction Add-on (jss_NN-1.0.jar - select one matching your JIRA version);
Copy Plugin JAR and Add-on JAR to JIRA_HOME/plugins/installed-plugins;
Unzip initial Jython scripts from jss_base_scripts.zip to JIRA_HOME - it will create jss folder in JIRA_HOME;
Modify /WEB-INF/classes/actions.xml:
- JIRA 4.0.x and 4.1.x: change "issue.EditSubTaskIssue" to "com.quisapps.jira.plugin.action.EditSubTaskIssue" and "issue.EditIssue" to "com.quisapps.jira.plugin.action.EditIssue"
- JIRA 4.2, 4.3 : change "issue.EditIssue" to "com.quisapps.jira.plugin.action.EditIssue"
Restart JIRA

Prerequisites: Jython 2.5.0 installed, python.home Java property set for JIRA and /WEB-INF/classes/actions.xml patched;
Download JSS 1.1 Plugin JAR (jss-1.1.jar), Initial scripts package (jss_base_scripts.zip) and On-edit Validator & Postfunction Add-on (jss_NN-1.0.jar - select one matching your JIRA version);
Replace old jss-NNNN.jar with new Plugin JAR and Add-on JAR in JIRA_HOME/plugins/installed-plugins;
Make a backup copy of your scripts library in JIRA_HOME/jss/jython and update initial Jython scripts from jss_base_scripts.zip to JIRA_HOME; you may safely choose to not overwrite any existing files.
Restart JIRA

All your existing scripts are compatible with new JSS version.