Good policy - you don't want to mess with the PTC folder as it can cause big problems when updating. The "My Arbortext" folder can be setup very simply by configuring the APTCUSTOM environment variable to point to the folder location. You can then copy over the "custom" folder contents from the original PTC folder. This will act as a template for the folder structure of your "My Arbortext" folder. If you ever move to a new machine, just copy over the "My Arbortext" folder and setup the APTCUSTOM again on the new machine.
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