I'm looking for an online inventory management application *opensource/freeware* that I can use to allow my stores to load their inventory at night and it tracks the amount sold, item sold, if the differences are correct... things like that.

If anyone knows of anything like this please let me know.

You're asking if there is an open source solution to an enterprise script that corporations pay thousands to get a perpetual inventory system?

Have you looked into Google Merchant and Open Cart? Using both together (they have a $45 OpenCart plugin that integrates with GMerchant) may achieve the results you want.

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