Make many seldom-used generalized variables obsolete

Make many seldom-used generalized variables obsolete

The vast majority of these are unused in-tree, and many of them
perform actions that aren't obvious when reading the code.

* lisp/server.el (server-ensure-safe-dir): Prefer with-file-modes
over letf-ing default-file-modes.
(server-start): Ditto.

* lisp/winner.el (winner-set-conf): Don't use generalized variable
window-height.

* lisp/emacs-lisp/gv.el: Make most little-used generalized
variables obsolete.

* lisp/org/oc-basic.el (org-cite-basic--set-keymap): Adjust
buffer-substring generalized variable usage.