Nexus 7, Ubuntu 12.04, Eclipse Juno
Nexus 7 has been set developer mode. And in Eclipse I can see lists in "File Explorer" for Android.
I can see storage/emulated/legacy
But I can not see storage/emulated/0/ folder
I have had the same problem as well. Found the answer in a comment on a seperate stack overflow question so credit goes to the author.
everything is a link to /storage/emulated/legacy anyway, which itself is a link to /mnt/shell/emulated/0 which contains the file. – moonlightcheese Dec 7 '12 at 13:55
So check out that directory through the Android file explorer, and you will have your files.
Edit: Here is a link to the original comment: Nexus 4 not showing files via MTP