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You need to be really careful about a few of those options. Please take a look at the upgrade to get a clear understanding of what these options will do. For example, the following property if set to ALL TEAM MEMBERS will add everyone to the new Collaboration Manager role. In my case, I did not want this, thus I used ONLY_ROLE. This kept the team roles as they were in the previous version.
<property name="<b">com.ptc.windchill.upgrade.templatemigration.collaboration.option" targetFile="codebase/wt.properties" default="ONLY_ROLE"/>
Sorry, mistakenly hit OK in the middle of typing on last post
I also setthis property to true,
<property name="<b">com.ptc.windchill.upgrade.directives.migrator.verbose" targetFile="codebase/wt.properties" default="true"/>
I recommend reading the upgrade guide on this section, and ensure that you have a clear understanding of what these properties control.
Here is the task list that I created. Some may not apply to you and needs to be updated based on you configuration and customizationsbut I hope it helps you out. I've used this on numerous upgrades.
You should also consider changing the memory allocation to atleast 1 GIG within the $WT_HOME/bin/UpgradeManager.sh to do this you need to add this in your site.xconf:
wt.upgrade.tools.java.args="-Xms1024 -Xmx2048m"