This fixes user environment setup for sessions which doesn't successfully go
through a shell init.
Note we don't go through `sessionVariables` as we want the wrappers to have
highest priority. It would also cause wrapperDir to occur twice when in shell
sessions, as shells use `sessionVariables` too while prepending wrapperDir in a
custom snippet.
In particular logging in and out of gnome-shell could result in a broken path
without this fix.
We were only replacing them in the profiles. We also need to do this in
the values of variables, including both the session-relative variables
and the non-session-relative variables.
