It is the apocalypse after all.

There one non-tedious way to do this; right now by event you can only remove a single item at a time (i.e. quantity 1) with event command 81, so you would need to use it 255 * 99 times.

So you'll need instead to code a new event command you would use at the beginning of WoR event. There are unused event commands in FF6. This command would just set the whole inventory SRAM range to a bunch of 00 (or w/e a clear inventory is, you can know by viewing the inventory RAM in a debugger at the game start). For that you need to learn some assembly coding. The wiki has the info about the RAM addresses for the inventory.

You can first in your WoR start event unequip Celes with an existing event command, use your custom event command then subtract all the gil from the inventory. Event command 85 can subtract 0xFFFF gil from inventory, so use it as many times in a row as you need to reach the maximum amount of gil possible to have in FF6. You could also set the amount of gil in saved RAM to 0 in your custom inventory event command before or after clearing the inventory.