Would it be possible to use Chromeless to tell the operating system to have a specific file opened by its default native application? So you could have a collection of links in a Chromeless app, that represent files on the user's computer, and the user could click a link for say an Excel file, and Excel would launch and show the file? Ideally this is what the new FileSystemApi needs, so that a web-based "dropbox" becomes possible. At the moment, any kind of web-based file manager must result in downloads to get most files opened, and re-uploads, whenever the user changes the file.
