Always stored in the cookies directory -- it has to be this way because it's the one part of the users' computers that you (the developer) have access to by default. All other areas of the users' hard drives are restricted.
And even then, you don't really have "access" per say. You can ask for a cookie, and the one that your site (or another friendly site) wrote to the user's computer is returned. It's a very restricted access.
You can present the user with a list of the cookies that you have written, but you don't have access to the other ones on their computer.
There are sites that collaborate to share these cookies, and access to them, but it's a very dirty practice, and it's what gives cookies such a bad name. So just stick to the ones that you have 'legal' access to.
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