Move define-obsolete-variable-alias before the var's definition.
* lisp/vc/log-edit.el (vc-comment-ring, vc-comment-ring-index):
* lisp/tooltip.el (tooltip-hook):
* lisp/textmodes/reftex-toc.el (reftex-toc-map):
* lisp/textmodes/reftex-sel.el (reftex-select-label-map)
(reftex-select-bib-map):
* lisp/textmodes/reftex-index.el (reftex-index-map)
(reftex-index-phrases-map):
* lisp/speedbar.el (speedbar-syntax-table, speedbar-key-map):
* lisp/progmodes/meta-mode.el (meta-mode-map):
* lisp/novice.el (disabled-command-hook):
* lisp/loadhist.el (unload-hook-features-list):
* lisp/frame.el (blink-cursor):
* lisp/files.el (find-file-not-found-hooks, write-file-hooks)
(write-contents-hooks):
* lisp/emulation/tpu-edt.el (GOLD-map):
* lisp/emacs-lock.el (emacs-lock-from-exiting):
* lisp/emacs-lisp/generic.el (generic-font-lock-defaults):
* lisp/emacs-lisp/chart.el (chart-map):
* lisp/dos-fns.el (register-name-alist):
* lisp/dired-x.el (dired-omit-files-p):
* lisp/desktop.el (desktop-enable):
* lisp/cus-edit.el (custom-mode-hook):
* lisp/buff-menu.el (buffer-menu-mode-hook):
* lisp/bookmark.el (bookmark-read-annotation-text-func)
(bookmark-exit-hooks):
* lisp/allout.el (allout-mode-deactivate-hook)
(allout-exposure-change-hook, allout-structure-added-hook)
(allout-structure-deleted-hook, allout-structure-shifted-hook):
* lisp/dirtrack.el (dirtrack-toggle, dirtrackp, dirtrack-debug-toggle)
(dirtrack-debug): Move call to define-obsolete-variable-alias so it
comes before the corresponding variable's definition.
Update docstrings and comments to use "init file" terminology.

* bookmark.el (bookmark-bmenu-toggle-filenames): Doc fixes.
* comint.el (comint-prompt-read-only):
* custom.el (defcustom):
* hi-lock.el (hi-lock-mode):
* ibuffer.el (ibuffer-formats):
* ielm.el (ielm-prompt-read-only):
* novice.el (disable-command):
* saveplace.el (toggle-save-place):
* speedbar.el (speedbar-supported-extension-expressions):
* startup.el (auto-save-list-file-prefix, init-file-user)
(after-init-hook, inhibit-startup-echo-area-message):
* strokes.el (strokes-help):
* time-stamp.el (time-stamp):
* calendar/calendar.el (calendar, diary-file):
* calendar/diary-lib.el (diary-mail-entries, diary)
(diary-list-entries-hook):
* calendar/holidays.el (holidays, calendar-holidays):
* calendar/lunar.el (lunar-phases):
* calendar/solar.el (sunrise-sunset):
* emulation/edt.el (edt-load-keys):
* emulation/viper.el (viper-mode):
* eshell/em-alias.el (eshell-command-aliases-list):
* eshell/esh-util.el (eshell-convert-numeric-arguments):
* international/ogonek.el (ogonek-information):
* net/tramp-cmds.el (tramp-bug):
* net/quickurl.el (quickurl-reread-hook-postfix):
* play/decipher.el (decipher-font-lock-keywords):
* progmodes/cc-styles.el (c-set-style):
* progmodes/idlw-shell.el (idlwave-shell-prompt-pattern):
* progmodes/inf-lisp.el (inferior-lisp-prompt):
* progmodes/octave-mod.el (octave-mode):
* progmodes/sql.el (sql-mode, sql-interactive-mode, sql-password):
* progmodes/verilog-mode.el (verilog-read-defines):
* textmodes/two-column.el (2C-mode): Likewise.
Update copyright notices for 2013.
Auto-commit of loaddefs files.