Here is your answer. DON'T.
You have only 1 place to change your file references and that's in the export dialogue options. Once exported don't change anything. You might want to, but don't.
1. Everytime you export you will need change the sorting of the files.
2. c2runtime.js has already defined and mapped where those files are located. Moving files will break that.
3. To update the c2runtime.js will need to be updated every export.
4. You will likely break things.
When does anyone go into say a game like Mass Effect and start re-orginizing files?
If you are creating a website front end you don't need to re-orginize the export files.
Create your website front end view. In your html page use an iFrame. Refer to the game index.html into the iFrame.
there you go. no need to change the exported files. Your just going to make your life harder if you go the other way.