About ten years ago I was involved in a project to develop a software tool to help manage FDA 10k compliance for a Type 1 medical device (a device that comes in physical contact with a patient). It makes HACCP look like child's play. You have to have a written process in place that talks about how you document meetings where any product design decision even gets discussed incidentally. If you decide to change the company you source grub screws from you have to document that so that, if somehow the grub screw gets implicated in a patient safety report, you can figure out the who, why, where, how, and when the decision got made. FOR EVERYTHING.
While it's not necessary to go to these lengths, it makes a good deal of sense to have such a manual and to keep it up to date. It's exactly the sort of thing that inspectors - and insurance companies - love. A good plan could help you reduce insurance premiums.
First step: There is a manual. The first chapter (chapter zero, traditionally) in the manual talks about why there is a manual in the first palce, how to use it, who it covers, how training is done, how the efficacy of training is measured, and more.
In each chapter there is a revision history for the contents of the chapter. Everyone whose work is covered by that chapter has to sign off they they read the chapter, that they received the proper training, and that they understand what it means and how it has an impact on their work. Do not throw away pages that are outdated! There's a section in each chapter for deprecated pages, if there's an issue the inspector will want to see what changed.
One of the chapters covers cleaning procedures. Another avoiding cross-contamination. Another about the process of accepting beans and testing them when they come in. There's a separate chapter that is a compendium of test results (e.g., aW, cut tests on acceptance). Have everyone sign off on the fact that they received the proper training and know what to do. Of course, you need to actually do the training.
Keep the manuals in a prominent place and make sure the inspectors know where they are when they show up - and that they can see how serious you are about these issues.
Keep in mind also that if you are manufacturing chocolate from cocoa beans in the US that the FDA has some specific guidance for inspectors. Whatever you do (at least here in the US) this is basic stuff that you need to make sure you're paying attention to. One particular requirement is the use of magnets to remove metal in the pre-cleaning step, something that is often overlooked.
-- edited for typos and grammar --
clay - http://www.thechocolatelife.com/clay/
updated by @clay: 02/25/15 04:18:55PM