Whenever you make a change, of any kind, that will affect the URL layout of the site, you must flush the rewrite rules one time.
Easiest way to do this: In the wp-admin, visit the Settings->Permalinks page. You don’t even have to save changes, just load that page.
The act of loading the Permalinks page causes the rewrite rules to be flushed and rebuilt. Since your CPT is now active, it will be included in the new rules that will be built and saved to the database.
Edit: Sorry, I misread your original problem.
It seems that you’re wanting it to use the “archive-packaged.php” template with the URL of http://[websitehere].com/packaged-foods/organic-wines/.
The reason this isn’t working is because “packaged-foods” is a taxonomy, not your custom post type. See, archive-* templates work with CPTs. Taxonomy templates fall under the taxonomy-* templates. And your pretty URL here doesn’t specify a custom post type at all.
Use the taxonomy-pf_groc_cat.php template instead.