This is purely the cause of the shell having a builtin pwd command that displays a path that is consistent with the argument to the "cd" command that was typed to enter the directory, not the actual path you're in. The shell does this to provide a consistent view for the user when following symlinks.
You can always type /bin/pwd to avoid this and you'll always get the correct path.
> You can always type /bin/pwd to avoid this and you'll always get the correct path.
Yes, but it affects other programs as well. See the `cat myFile` example in the gist.