File Upload and knowing the directory structure

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We are using jquery fileupload to drag and drop files (and folders) from a local computer to a browser. This works great but we can't capture the directory structure of the files within the folder. I understand why (from a security perspective and javascript) this doesn't work, but does anyone have any thoughts on best ways to achieve the same thing.

Again, I want my customer (internal app) to drag and drop a folder into my application. My application can see the list of filenames and they get uploaded, but I would like to maintain the directory structure of those files for use elsewhere. i.e., it's important for me to know that it came from directory x/1/a rather than y/2/b.

Thanks in advance!

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