Firstly Manager can do everything that you require. In this post an overview will be provided
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It can handle all your Inventory requirements including both Raw Materials and Finished Goods (food products). Inventory has a basic mode and a more complex mode. In the basic mode you just use the Purchase Invoices & Sales Invoices tabs. For the more complex mode you would also use the Goods Receipts and/or the Delivery Note tabs.
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To convert raw materials into food products you would use the Production Orders tab, this process will automatically adjust your Inventory levels.
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The raw materials and finished goods Inventory can be reported on the Balance Sheet either together or separately.
You didn’t say, but does the manufacturing unit “sell” to the retail shop and the does the retail shop also need to record it sales / inventory.