Why don't you use Koll3ctions?
It's free. You can download here:
Create collections for books on Kindle automatically based on the Kindle folder structure.
Runs on Mac OS X, Linux and Windows. (It's platform independent.)
Supported file formats: azw, azw1, mobi, pdf, prc, tpz, txt, cbz, zip, aa, aax, mp3
Find the kindle automatically.
Command line support for advanced users.