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Modified pos.conf.pl overwritten during upgrade

I know with files from ledgersmb/bin or ledgersmb/scripts directories, I can create custom versions of these files and place them in the corresponding custom directory (i.e. ledgersmb/bin/custom) so that they get executed in place of the stock version and also during upgrades they don't get overwritten.  Is there something similar for files in the root directory (i.e. ledgersmb) such as for pos.conf.pl?  I realized that after my upgrade today that my modified version of pos.conf.pl was overwritten so wanted to see how best to handle this situation.

Best Regards,
Steven Marshall