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We use virtual server for our development\test boxes, and I had the system admin clone one of test Windchill servers along with the Oracle database server. What is considered the best way for these cloned servers, using the PTC Rehosting software, or simply making the changes through the various configuration files?
I'd say through the rehosting tool. It manages not only .xconf changes but also changes to the database, ldap and maybe more (can't remember exactly it's been a while since I had my hands on it)
True "cloning" ends up with the same hostname - can't have on the same domain.
The Re-host utility allows for updating all the configurations and data.