Yifan, thanks for all your work.
I believe that you are using a Mac because all your hacks create additional files on the Kindle which are not needed/used on Windows/Linux.
For every file "file.ext", that your tools create, another hidden one "._file.ext" is created. I also found some .DS_Store folders. These files are used to store customizations for the Mac Finder.
For more information check this Wikipedia article.
http://en.wikipedia.org/wiki/.DS_Store
Please update your tools so that they will not add these files.