Sorry this is late... but I totally agree with YoGi. The Apache Commons package will make it too easy as all the heavy lifting is already done for you. Your post recently shows that you're more than familiar with representing files as links on a page so now all you have to do is allow your users to drag and drop the files to a text area (with an alternative 'browse' button for grabbing other files from their hard drive) and then using the commons package to do the uploading.
Sorry this is late... but I totally agree with YoGi. The Apache Commons package will make it too easy as all the heavy lifting is already done for you. Your post recently shows that you're more than familiar with representing files as links on a page so now all you have to do is allow your users to drag and drop the files to a text area (with an alternative 'browse' button for grabbing other files from their hard drive) and then using the commons package to do the uploading.