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I believe the installation zip here:
https://www.altera.com/content/dam/altera-www/global/en_us/support/boards-kits/arriav/arriavst_5astfd5kf40_soc_v15.1.0b185.zip should have a "golden_top" folder (or something like that) which has all the pins on the board defined (with the correct pin location)
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Certainly, this contains all the appropriate files to start with the "bare-metal" design,
or you may also check in Google: bare-metal gold designs.
:)
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Alex