I'm supporting this. The policy files should be preserved in /etc.
We had a (late) upgrade from Etch to Lenny. On Etch we were already using a backport.org version of Java6. So for us it was just a minor version upgrade to Lenny.
Developers replaced the policy files at some time in the past for their application. When we upgraded the system, the application failed and for hours we were searching for the fault...
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