what is gvfs for and what are the read/write permissions on those files and why can not some be changed

Hi, @Semih !

If you try command below (from "Terminal"), you should see something like this :

dzejar@Xubuntu-14v04 : ~ $
dzejar@Xubuntu-14v04 : ~ $ ps auxwOp | grep gvfs
dzejar 2647 0.0 0.2 202844 5556 ? Sl avg30 0:00 /usr/lib/gvfs/gvfsd
dzejar 2654 0.0 0.2 419580 4656 ? Sl avg30 0:00 /usr/lib/gvfs/gvfsd-fuse /run/user/1000/gvfs -f -o big_writes
dzejar 3018 0.0 0.4 305316 8536 ? Sl avg30 0:03 /usr/lib/gvfs/gvfs-udisks2-volume-monitor
dzejar 3030 0.0 0.3 218800 6156 ? Sl avg30 0:00 /usr/lib/gvfs/gvfs-gphoto2-volume-monitor
dzejar 3034 0.0 0.2 206508 5576 ? Sl avg30 0:00 /usr/lib/gvfs/gvfs-mtp-volume-monitor
dzejar 3038 0.0 0.3 292172 6220 ? Sl avg30 0:00 /usr/lib/gvfs/gvfs-afc-volume-monitor
dzejar 3048 0.0 0.3 693488 6544 ? Sl avg30 0:00 /usr/lib/gvfs/gvfsd-trash --spawner :1.19 /org/gtk/gvfs/exec_spaw/0
dzejar 13456 0.0 0.3 132108 6552 ? Sl 03:41 0:00 /usr/lib/gvfs/gvfsd-metadata
dzejar 27337 0.0 0.1 22136 2564 pts/16 S+ 15:14 0:00 grep --color=auto gvfs
dzejar@Xubuntu-14v04 : ~ $

 => which means that your Ubuntu system functions well.

If you then try another comannd, and see :

dzejar@Xubuntu-14v04 : ~ $ dpkg-query -l gvfs*
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture Description
+++-=========================-=============-=============-========================================
ii gvfs:amd64 1.20.3-0ubunt amd64 userspace virtual filesystem - GIO modul
ii gvfs-backends 1.20.3-0ubunt amd64 userspace virtual filesystem - backends
un gvfs-backends-goa <none> <none> (no description available)
ii gvfs-bin 1.20.3-0ubunt amd64 userspace virtual filesystem - binaries
ii gvfs-common 1.20.3-0ubunt all userspace virtual filesystem - common da
ii gvfs-daemons 1.20.3-0ubunt amd64 userspace virtual filesystem - servers
ii gvfs-fuse 1.20.3-0ubunt amd64 userspace virtual filesystem - fuse serv
ii gvfs-libs:amd64 1.20.3-0ubunt amd64 userspace virtual filesystem - private l
dzejar@Xubuntu-14v04 : ~ $

 => again, all is OK.

This is (if I could remember corrextly) so-called Gnome (?) Virtual File System - hence gvfs ...
That's libraries / daemons / etc. which helps you to *JUST* clck on any HDD / Partition in your File Manager and you have mounted and accesed HDD / Partition. As you see, I still use 14.04. Based on your Ubuntu version, the package versions will be different.

If you have installed Synaptic Package Manager, you could search for "gvfs" and see more detail.

Just to remember you, when usung USB sticks or USB racks for HDDs, you should first, in your File Manager, do the *RIGHT MOUSE CLICK* and do the UN-mounting. The GVFS is responsible for mounting the NTFS/FAT/SMB (via fuse) and all Linux filesystems, and un-mounting, of course...

The "/run/user/????/" directories are system's care directories, and you should not touch them...

Hope this helps!