Recover GoodReader data after iOS 7 upgrade?
This is not exactly answering to my own questions. But for those who knows programming, there is a way to get away with it. For me, I wanted to restore all photos I put in my GoodReader.

I get into the backup directory. Used the bash command:

ls * | xargs file {} | grep image\ data &gt; /Desktop/backup.txt

to list all files and it was printed like this (the first few rows):

2:0006c6f73a741907373e2eabcb3763bebf17bdc8: PNG image data, 25 x 15, 8-bit/color RGBA, non-interlaced
3:000bb4a992491782ef65642e1298244242883c66: JPEG image data, EXIF standard 2.21
4:001c384e486a787bb376cee192ee763858e00274: JPEG image data, EXIF standard 2.21


Then I am using Python to rename those files back to Jpeg or PNG files. There are not the same names as they were originally but this has been good enough. There is a Manifest.mbdb file in the same backup directory. I didn't have much time digging into it but this file looks like to contain information which one can use to restore all information.