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Unfortunately, you cannot upload folders, the File Upload field only captures files individuality as their file type extensions are being checked, but you can have a workaround and have it more organized. If you are looking on how to upload them to Dropbox, here's what you can do:
1. First, add a text box to where your users will let you name the folder where the uploaded files will be. Add the File Upload field and enable the "Allow Multiple".
2. After that, you can integrate your Dropbox to the form, here's a guide: http://www.jotform.com/help/77-Upload-to-Dropbox-with-JotForm
3. In your Dropbox settings, set the path and folders on how the form's data will be uploaded in your Dropbox folder.
4. In the screenshot above, I set the "Submission Folder Name" to fetch the text box that will be the custom folder name.
The path in my case will be this one:
Dropbox root/Upload Folders Text/Name Your Folder For the Uploaded Files
5. However, please do take note that when the folder name is the same, it will replace or update the existing ones. So I would advise that you create a specific path using unique ID to folder names, here are the tutorials that might help:
I hope that helps. Do let us know if you need more information on this.