This is the log from out most recent upgrade of Jira and Confluence

Download confluence-1.4.1.zip
Download atlassian-jira-enterprise-3.2.1.zip
Unpack both into D:\java

Run export on bugs.freehep.org and jira.slac.stanford.edu
d:\fh-jira-15jun2005.zip (902 kB)
d:\slac-jira-15jun2005.zip (2564 kB)
Turn off tomcat service

Backup confluence directory
d:\ConfluenceData -> d:\Copy of ConfluenceData

To be extra safe, also back up MySQL databases using phpMyAdmin

Upgrade Jira using instructions at:
http://atlassian.com/software/jira/docs/v3.2.1/upgrading.html

SLAC-Jira

Edit entityengine.xml, only change is datasource name hsql -> mysql, and
jndi-name->java:comp/env/jdbc/SLACJiraDS
AND name="java:comp/env/UserTransaction" (X2)

Run build.bat

In D:\java\tomcat-base2\conf\Catalina\jira.slac.stanford.edu edit ROOT.xml
Change to use url="jdbc:mysql://localhost/slacjiradb?autoReconnect=true"
Drop all tables in slacjiradb using phpMyAdmin

Unpack dist-tomcat war files into D:\java\tomcat-base2\slac-jira-apps\ROOT

FreeHEP-JIRA

Edit entityengine.xml again, change jndi-name->java:comp/env/jdbc/JiraDS

Run build.bat

In D:\java\tomcat-base2\conf\Catalina\bugs.freehep.org edit ROOT.xml
Change to use url="jdbc:mysql://localhost/fhjiradb2?autoReconnect=true"

Unpack dist-tomcat war files into D:\java\tomcat-base2\bugsapps\ROOT

Upgrade Jira using instructions at:

http://confluence.atlassian.com/display/DOC/How+to+update+Confluence

Edit confluence-init.properties in D:\java\confluence-1.4.1\confluence\WEB-INF\classes
Add: confluence.home=D:
ConfluenceData

Edit: D:\java\tomcat-base2\conf\Catalina\confluence.slac.stanford.edu\Root.xml
Point docBase=D:/java/confluence-1.4.1/confluence
Change to point to slacjiradb (for authorization)

Delete old stuff in D:\java\tomcat-base2\work\Catalina

Restart tomcat, and load backed up data into JIRA

copy old osuser.xml into confluence\WEB-INF\classes