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You could certainly do that, but you'll want to be careful as you do--there are HTML files in the WebHelp folder that refer to those JS files, too. That means you'd either have to move all of those into the scripts folder or amend all of the <script> tags in those files so they point to the right location.
If you move all of those files into the scripts folder, you'll have to check the start page (I think the same as what you called the launch page) for any references to those files so you can update the paths. Depending on how many there are and whether the start page changes each time you generate, you may not have much trouble.
After you move things and verify that the help isn't broken, you may want to consider using the publish feature to publish to a second location on your hard drive after you generate. This would help ensure that the changes you've hard-coded into your files aren't overwritten in that second location every time you generate. Then you use the files in the second location to launch your help to the users.
So the basic answer to your question is yes, but you will probably have to do some experimenting first to make sure all references are correct.
If I understand what you're saying, though, you're talking about putting a scripts folder within the WebHelp folder? In that case, wouldn't the reference be src="scripts/whver.js"? Or is your start page not directly within the WebHelp folder?
Thanks for your response. The start / launch page is within the Webhelp folder; however, we may have to move the files (security purposes) to a different directory.
Definitely not for the faint of heart!
Just something to ponder... Rick