Files and folders are visible on computer, but NOT visible on Android's file explorer I have Nexus 6 running on Lollipop. I am seeing folders in Android File transfer on the computer which are apparently not real, or at least not visible on the phone in file explorer.

Here, you see the "Music" folder on PC,



But not on Android,



In addition to seeing the folder only when I look from the computer. This seems to be the opposite problem everyone else has. What is going on here?
It's due to a difference in permissions.  

When you are looking from the computer, you are accessing the phone over ADB or MTP, which is likely running with special privileges, such as 'shell' or 'root'. When you are looking from the app on the phone, you are running as a certain Android 'userId' and 'appId' in a sandbox which does not necessarily have access to other user's files or many system files. In fact, Android 4.2 and later uses file namespaces and bind mounts to make other user's files completely invisible (not even mounted) when another user is logged in. Even a root file explorer will not see unmounted files.

The only way to see all system files is to be running as root. The only way to see all of a particular user's files on external storage is to be logged in as that user, thus forcing the system to mount the appropriate external storage folders.