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Files appear in MTP interface, but not in file manager or adb

So, I got my Galaxy Nexus for Christmas. Unlocked the bootloader and rooted it right away. Now I am trying to copy files from my old Droid 1's SD card. So, I copied everything off of the SD Card onto my computer and then proceeded to copy files onto the Nexus using the MTP interface.

Some of the things I have copied are available on the phone. For example, most of the pictures, and a video and some MP3 files that I didn't put onto Google's music service are all on the phone. I can see them with the File Manager app as well as accessing them through the Gallery/Music/Video players.

I have a folder called Media, which has two sub folders Video and Audio. The Video folder has all of the files and sub-folders correct, but the Audio folder is messed up.

In the MTP interface, the Media folder shows the Audio sub-folder and all of the folders and files underneath it. However, on the phone the Media folder has the Audio folder as 'audio' (note it is lower case and not upper case as it should be) and under 'audio' is only a 'notifications' folder, with only one file in it. I can also see this by using adb to access the shell.

Any thoughts?
 
Ok, so as soon as I finish entering my question, I think I got my answer.

There were two folders in /mnt/sdcard directory: Media and media. And, since Windows is still too $%#^@$@ to notice the difference between upper and lower case letters it must have done some strange merging on the two folders.
 
Well, now I seemed to have really hosed it up.

I tried to get rid of the now empty 'media' folder and it wouldn't let me (this is via the adb shell). Kept saying that it wasn't empty. So I renamed it (mv media Thing). After I did that, I couldn't access the Media folder any more.

shell@android:/mnt/sdcard $ ls Media​
opendir failed, No such file or directory​
1|shell@android:/mnt/sdcard $​

An ls shows that it is there:

shell@android:/mnt/sdcard $ ls -l​
drwxrwxr-x root sdcard_rw 2011-12-25 18:57 Alarms​
drwxrwxr-x root sdcard_rw 2011-12-25 18:57 Android​
drwxrwxr-x root sdcard_rw 2011-12-25 21:00 DCIM​
drwxrwxr-x root sdcard_rw 2011-12-25 18:57 Download​
drwxrwxr-x root sdcard_rw 2011-12-25 22:31 Icons​
drwxrwxr-x root sdcard_rw 2011-12-26 11:48 Media​
drwxrwxr-x root sdcard_rw 2011-12-25 18:57 Movies​
drwxrwxr-x root sdcard_rw 2011-12-25 22:41 Music​
drwxrwxr-x root sdcard_rw 2011-12-25 19:00 Notifications​
drwxrwxr-x root sdcard_rw 2011-12-25 21:04 Pictures​
drwxrwxr-x root sdcard_rw 2011-12-25 18:57 Podcasts​
drwxrwxr-x root sdcard_rw 2011-12-25 18:57 Ringtones​
drwxrwxr-x root sdcard_rw 2011-12-25 21:59 SMSBackupRestore​
drwxrwxr-x root sdcard_rw 2011-12-25 22:13 TitaniumBackup​
-rw-rw-r-- root sdcard_rw 1 2011-12-25 18:56 cfg_dun_status​
-rw-rw-r-- root sdcard_rw 1 2011-12-25 18:56 cfg_uart_sel​
-rw-rw-r-- root sdcard_rw 1 2011-12-25 18:56 cfg_usb_sel​
drwxrwxr-x root sdcard_rw 2011-12-25 22:16 com.google.android.apps.listen​
drwxrwxr-x root sdcard_rw 2011-12-25 22:25 data​
drwxrwxr-x root sdcard_rw 2011-12-25 22:28 drocap​
drwxrwxr-x root sdcard_rw 2011-12-25 22:30 games​
drwxrwxr-x root sdcard_rw 2011-12-25 21:13 handcent​
drwxrwxr-x root sdcard_rw 2011-12-25 22:43 phonePrioritizer​
drwxrwxr-x root sdcard_rw 2011-12-25 21:08 tapatalkdrodiforums_download​
drwxrwxr-x root sdcard_rw 2011-12-25 22:45 twc-cache​
drwxrwxr-x root sdcard_rw 2011-12-25 21:02 u1​

I also noticed that the /data/media directory seems to be the same thing as the /mnt/sdcard folder and that is probably because the /mnt/sdcard is actually a FUSE file system.

So, any thoughts how I can clear this up without having to do a factory reset and start all over again?
 
I think it was the Media/media issue. Using adb, I became root and went into the /data/media directory. I cleaned up the Media folder there and then was able to copy the files using MTP after rebooting the phone.

So, the moral of this story -- watch out for folders that differ only in the case of their names.
 
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