Initially I thought this was a problem with Google Play / Apollo, but I realize now that when I plug in my phone via USB, I can't see any of the many, many folders and files present on /sdcard that I could see previously.
If I copy a "new" mp3 onto my Galaxy Nexus, it's recognized just fine by both Google Play and Apollo. However, none of my old mp3s are recognized. They were placed in /sdcard/Music, a folder that I cannot see when I plug in my phone, only from the file manager running on the phone. The issue persists if I move an "old" mp3 from my music folder out into the sdcard root, it's still not recognized. This makes me think this might be permission related, but the file manager says that all files are readable and writable.
I've tried running "fix permissions" in both ROM manager and the CWM recovery, but it makes no difference. Any idea what has happened, and how to fix it so that I can use all my old files again? :)
edit If it's any help, I just ran ls -al in a terminal emulator and I can't see any difference at all between folders I can and cannot see. Example: I can see /sdcard/media just fine, because I created that folder from Explorer in Windows. Music in that directory works. I cannot see /sdcard/music. Here's the permissions:
drwxrwxr-x root sdcard_rw 2012-09-18 media
drwxrwxr-x root sdcard_rw 2012-09-16 music
This is a bit confusing.
edit2 When I try pulling and pushing a file with adb like so:
adb pull file.tar
adb push file.tar file2.tar
I get
failed to copy 'file.tar' to 'file2.tar': Read-only file system
As bk201doesntexist on the XDA forums pointed out, this is because you have to use an absolute path. However, when I do adb push file.tar /sdcard/file.tar the file gets transferred, shows up when i run ls, but it's invisible in the "Galaxy Nexus" unit in My Computer in Windows.
tl;dr When I push files with adb push they get transferred but don't show up in the "Galaxy Nexus" unit in My Computer. "Old" files from before ROM-switching do not show up. New files that I put in now work fine.
Answer
As a final resort, I tried doing a full wipe and reinstalling CM10 M1 completely, without restoring any settings or apps from any old installations. The issue still persists! Any files created with my now "old" CM10 installation no longer appear, even when they are moved within a folder where other "new" files are shown and working. Switching back to AOKP also did not solve the issue, so the issue does not only persist over reinstalls of CM but also across ROMs.
What finally solved this issue for me was reformatting my /sdcard partition with the newest version of CWM Recovery. This might not be a very clean solution, but in my case I needed to clean up the sdcard anyway.
If formatting isn't an option, try the other answer posted here regarding .nomedia files, I had no success with it as I was unable to find those files.
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