Which directories does the Media Scanner scan?
Media Scanner scans both SD card as well as USB storage, but not ROM and system storage. Means, it scans from /sdcard/ and /sdcard/external_sd/ mount points. It goes deep inside all non-hidden sub-directories, unless .nomedia file is detected.

Media Scanner skips ROM and system storage because both require root permission to write anything there. And, its very unlikely for an end-user to store music, photo there.