items.json contains the item definitions, with "id", "dispName", "animName", "aniFrame", and "desc" keys for each item. recipes.json contains recipe definitions, with ingredients (an array of item ids), and result keys for each recipe. They're different in form and function, which is why I used two files. It works the same if they're all together like they were in the original example.
On start of layout, the two files are loaded and placed into the "items" and "recipes" paths respectively, resulting in the exact same result as when it was just one file with items and recipes together. I've included that original file into the updated example (same link), if that way is preferable.
What do you mean only one has drag and drop enabled? If there were two of the same thing, how should which one be draggable be determined?
There are a few ways to ensure item (or recipe rather) order doesn't matter. The first way would be to not have conflicts to begin with. So don't have an A+B, B+C, or A+C recipe if A+B+C is a recipe.
Another way would be to use a different trigger to check recipes, like a button the user has to push (after adding items to a pot or something), so that it's not triggered immediately upon dropping. But even then order still kind of matters, you would probably just want check the bigger recipes first before the smaller ones.
You could also explicitly define a "priority" value in the recipe json, and check the recipes in order of their priority. But this is not much different than just leaving it as is - the priority is simply the order in which they appear in the recipe list.
One option would be to just not worry about it, and let the player figure it out. If you had A+B=C and A+B+C=D, they would have to add A+C before B or B+C before A to get D.