Stock Google Music app does not scan subdirectory in Android 4.2.1 Is it a bug in Jelly Bean 4.2.1 that subdirectories within the Music directory are not scanned for music files?
UPDATE: I just verified that copying using cp or using Nautilus on Ubuntu or Windows Explorer works just fine. They are scanned immediately by the player. But if I use rsync they are not! This is very strange. I also checked file permissions and they are the same in both cases.
I am trying to sync the music collection on my desktop to my Nexus 4. On my desktop my music is organized as follows.
    Artist1/
        Artist1/Art1_Track1.mp3
        Artist1/Art1_Track.mp3
    Artist2/
        Artist2/Art2_Track1.mp3
        Artist2/Art2_Track2.mp3
    ...

When I copy the same directory structure into the Music directory the stock music player does not scan the music in subdirectories. It works fine for files in the base Music directory though.
FYI, I use rsync to sync the music collection to the Music directory. I am using Android 4.2.1 Jelly Bean on the LG Nexus 4. The device is mounted using go-mtpfs on a Ubuntu installation.

Update: Some summary from the comments (by Izzy)

the problem only exists when files are transferred using rsync. While rsync is in progress, files get a temporary file name extension like e.g. .test.mp3.xdGHsk -- but they are correctly renamed to .mp3 once the transfer is finished (normal behaviour for rsync)
there are no .nomedia files in the affected directories
Rescan Media is used to force the Media Scanner to update the library after rsync completed its job

Update: More summary from the comments and correction (by Srinath)

USB connection mode is MTP, on the Linux PC the device is mounted using go-mtpfs (MTP file system implementation in Go language)
The files transferred using rsync can be viewed and played using a file browser app like ES File Explorer
If the problem is really that rsync renames the files, try rsync --inplace.