By Jeffrey Mcdaniel-Oracle on Dec 27, 2012
If there are any files in the \scripts directory that have been updated that you wish to keep as part of the ETL process the best way to do so is replace the template file to ensure those changes are not overwritten. Whenever replacing or updating a template always make sure to create a copy of the original file outside of the \etl folder. \scripts is an active, live directory. \etl\oracle\templates is the archived version of what is to be used in any further ETL processes if there are any configuration updates.
Also as of P6 Reporting Database 3.0 there is a directory called 'user_scripts' in the \scripts folder which is used for executing custom ETL additions. See P6 Reporting Database 3.0 Installation and Configuration guide for more information.