Hi Classic,
There is further detail on how this should potentially be considered within the Guidance Notes document.
As you're in the UK I'm assuming this is for UK/EU market?
It will depend on the products to an extent, but as a guide for our raw materials we've started with 1881/2006 and 396/2005 for specific contaminants, plus 2073/2005 on micro. For meat etc you may also want to consider the limits for veterinary residues.
For the packaging the guidance mentions contamination, malicious intervention and inappropriate materials - depending on the type of packaging and the product/process some of these may not be applicable, so I'd just document that so it's covered if challenged at audit. Don't see any issue with including migration within chemical contamination, but again I'd spell it out clearly that you're considering the food-contact packaging and the regulatory side here (e.g. 10/2011 for plastics), as it's always easiest to deal with the more pedantic auditors if you can clearly spoon-feed them the answers that they need