I'm sorry to tell you this, but I think you're out of luck for a few reasons:
1. NFC tags can only be accessed from a few cm awa. Most probably 5-10 folders would make up for those few cm (not including the signal absorbtion of the folders) and you woulnd't be abble to communicate with the deeper tags.
2. If you have two tags stacked, the phone wouldn't detect any of them. It will power both, both will start sending and the phone will not be able to understand any of them.
Sorry, but I think you'll have to find other sorting methods, but any that I could think of implies peoples' discipline.
Nokia 5110 > Alcatel OT303 > Nokia 3310 > Nokia 1100 > Nokia 1112 > Nokia 5000 > Nokia 6555 > Nokia 3120C > Nokia E51 > Nokia E52 > Motorola Defy > Galaxy Nexus
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