The Advanced Uploader is Java-based; this means that it will require your permission to access files. The Advanced Uploader will allow you to upload entire folders of files and include all of their content.
If you would like to use the Advanced Uploader:
Firefox on Mac OS X
Click Show Certificate (this will allow Firefox to always trust this applet) and then click Trust.
Firefox on Windows
Make sure that "Always trust content from this publisher" is checked if you do not want to be asked every time, and then click Run.