I've just done a clean install of Fedora 25 - clean all except the /home directories are on a separate disk/partition and are a carry over from the previous installation (F23). I added myself as a user and checked that the /home path contained my directory and my files and had the correct UID/GID (1000:100).

When I log in all goes well until I open a Terminal. At this point the prompt shows the current working directory as / not ~ as I would expect. 'ls -l' shows the path is actually / and the usual suspects are listed (dev, etc, sys, var, usr etc) all owned by root.

If iI then type 'cd' the prompt path does become ~ and my files are listed by 'ls'.

This is strange behaviour. Not something I've ever seen before (I've been using Linux since 1993 - kernel 0.99pl12)

The contents of my .bashrc and .bash_profile all seem to be normal. It would appear that the login process fails to set the correct path. The path in /etc/passwd is correct.

The environment variable $HOME is set correctly as even when the Terminal prompt is showing / as the path.

If I log in via ssh the prompt is ~ It only appears to be wrong in the Terminal window until I perform a 'cd'.

HOWEVER, if i create a new user using Settings -> Users the behaviour is normal. So the anomalous behaviour is something to do with the hold-over from my old F23 installation. The major difference between creating a new user and my old user is all new skeleton files that are added to the new home directory.

Anyone have any idea why this might be happening? It's driving me up the wall.

It's because the system is not adopting the holdover home directory as the new user's home. You might do

fstab needs to reflect change or address to partition of /home

along with what @AwesomeMachine said.

whenever I do this, because I keep my / (root) and /home separate

during install point it to /dev/sdxx /home no format
then create my user by the same name that is already there, it just says home/user name already there, no big deal, then give my user a password, log out of root then into my user no problem.

@BW-userx

Yep, fstab has just such an entry (except I use LABEL=/home to identify the disk/partition) and I do just the same as you during and after the install. I got the message about the home/user name already there. But unlike you when I logged out of root and into my account there is this problem!

@AwesomeMachine

The /home/user directory and all the files therein have the correct UID/GID already.

This problem only occurs when I use the GUI (presumably Gnome 3) NOT when I log in via ssh. What's the difference?

Well here's a strange occurrence. For unconnected reasons I set SELINUX=disabled in /etc/selinux/config and my problem has gone away!

If anyone can explain that I'd be very interested.

Thanks for all the suggestions AwesomeMachine & BW-userx.

Cheers

Chris

It looks like maybe you been put on the DOD list .. you know that LIST

more here
Security-Enhanced Linux

I'm glad you didn't have to jump through too many hoops and head aches before you got it fixed.

Probably SELinux has the other disk wrongly labeled. Try relabeling (see man selinux).
A check shows the context on my system is
/home home_root_t
/home/david user home directory
/home/david/* user data