bug#28001: 25.2; package.el is modifying init.el

[Marek Martin]

Please provide means for preventing packages from writing to init.el.
E.g. package.el adds this:
~/.emacs.d$ git diff                   
diff --git a/init.el b/init.el                          
index b2f97f7..77ee14e 100644                           
--- a/init.el                                           
+++ b/init.el                                           
@@ -1,3 +1,10 @@                                        
+                                                       
+;; Added by Package.el.  This must come before configurations of
+;; installed packages.  Don't delete this line.  If you don't want it,
+;; just comment it out by adding a semicolon to the start of the line.
+;; You may delete these explanatory comments.          
+(package-initialize)                                   
+                                                       
 (defun expand-dir-name (name &optional dir)            
   "Makes new directory name like this: '/dir/name/'.   
 Uses `file-name-as-directory' on `expand-dir-name' result."
@@ -76,3 +83,17 @@ Uses `file-name-as-directory' on `expand-dir-name' result."
                                                        
 (setq debug-on-error nil)                              
 (setq debug-on-quit nil)                               
+(custom-set-variables                                  
+ ;; custom-set-variables was added by Custom.          
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.  
+ '(package-selected-packages                           
+   (quote                                              
+    (which-key use-package undo-tree smartparens real-auto-save rainbow-delimiters org-plus-contrib intero helm-projectile helm-company haskell-snippets expand-region crosshairs cargo aggressive-indent ace-jump-helm-line))))     
+(custom-set-faces                                      
+ ;; custom-set-faces was added by Custom.              
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.  
+ )                                                     




In GNU Emacs 25.2.2 (x86_64-pc-linux-gnu, GTK+ Version 3.22.17)
 of 2017-07-31, modified by Debian built on trouble
Windowing system distributor 'The X.Org Foundation', version 11.0.11903000
System Description:    Debian GNU/Linux unstable (sid)

Configured using:
 'configure --build x86_64-linux-gnu --prefix=/usr
 --sharedstatedir=/var/lib --libexecdir=/usr/lib
 --localstatedir=/var/lib --infodir=/usr/share/info
 --mandir=/usr/share/man --with-pop=yes
 --enable-locallisppath=/etc/emacs25:/etc/emacs:/usr/local/share/emacs/25.2/site-lisp:/usr/local/share/emacs/site-lisp:/usr/share/emacs/25.2/site-lisp:/usr/share/emacs/site-lisp
 --with-sound=alsa --without-gconf --build x86_64-linux-gnu
 --prefix=/usr --sharedstatedir=/var/lib --libexecdir=/usr/lib
 --localstatedir=/var/lib --infodir=/usr/share/info
 --mandir=/usr/share/man --with-pop=yes
 --enable-locallisppath=/etc/emacs25:/etc/emacs:/usr/local/share/emacs/25.2/site-lisp:/usr/local/share/emacs/site-lisp:/usr/share/emacs/25.2/site-lisp:/usr/share/emacs/site-lisp
 --with-sound=alsa --without-gconf --with-x=yes --with-x-toolkit=gtk3
 --with-toolkit-scroll-bars 'CFLAGS=-g -O2
 -fdebug-prefix-map=/build/emacs25-Xmhbap/emacs25-25.2+1=. -fstack-protector-strong
 -Wformat -Werror=format-security -Wall' 'CPPFLAGS=-Wdate-time
 -D_FORTIFY_SOURCE=2' LDFLAGS=-Wl,-z,relro'

Configured features:
XPM JPEG TIFF GIF PNG RSVG IMAGEMAGICK SOUND GPM DBUS GSETTINGS NOTIFY
ACL LIBSELINUX GNUTLS LIBXML2 FREETYPE M17N_FLT LIBOTF XFT ZLIB
TOOLKIT_SCROLL_BARS GTK3 X11

Important settings:
  value of $LANG: en_US.utf8
  locale-coding-system: utf-8-unix

Major mode: Lisp Interaction

Minor modes in effect:
  subword-mode: t
  smartparens-strict-mode: t
  smartparens-mode: t
  show-paren-mode: t
  global-auto-revert-mode: t
  rainbow-delimiters-mode: t
  aggressive-indent-mode: t
  which-key-mode: t
  savehist-mode: t
  recentf-mode: t
  projectile-mode: t
  helm-mode: t
  async-bytecomp-package-mode: t
  crosshairs-mode: t
  column-highlight-mode: t
  global-hl-line-mode: t
  shell-dirtrack-mode: t
  helm-adaptive-mode: t
  override-global-mode: t
  tooltip-mode: t
  global-eldoc-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  column-number-mode: t
  line-number-mode: t
  transient-mark-mode: t

Recent messages:
Loading /home/marek/.emacs.d/Init/init-rust.el (source)...done
Loading /home/marek/.emacs.d/Init/init-savehist.el (source)...done
Loading /home/marek/.emacs.d/Init/init-scratch.el (source)...done
Loading /home/marek/.emacs.d/Init/init-undo-tree.el (source)...done
Loading /home/marek/.emacs.d/Init/init-uniquify.el (source)...done
Loading /home/marek/.emacs.d/Init/init-which-key.el (source)...done
Loading /home/marek/.emacs.d/Init/init-emacs-lisp.el (source)...done
Loading /home/marek/.emacs.d/Init/init-misc-post.el (source)...done
Loading /home/marek/.emacs.d/Init/init-keybindings.el (source)...done
For information about GNU Emacs and the GNU system, type C-h C-a.
zap-to-char: Wrong type argument: characterp, 134217848

Load-path shadows:
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/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ox-texinfo hides /usr/share/emacs/25.2/lisp/org/ox-texinfo
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-octave hides /usr/share/emacs/25.2/lisp/org/ob-octave
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/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-keys hides /usr/share/emacs/25.2/lisp/org/ob-keys
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/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-docview hides /usr/share/emacs/25.2/lisp/org/org-docview
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-perl hides /usr/share/emacs/25.2/lisp/org/ob-perl
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-pcomplete hides /usr/share/emacs/25.2/lisp/org/org-pcomplete
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-archive hides /usr/share/emacs/25.2/lisp/org/org-archive
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-sass hides /usr/share/emacs/25.2/lisp/org/ob-sass
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-w3m hides /usr/share/emacs/25.2/lisp/org/org-w3m
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob hides /usr/share/emacs/25.2/lisp/org/ob
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-id hides /usr/share/emacs/25.2/lisp/org/org-id
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-lilypond hides /usr/share/emacs/25.2/lisp/org/ob-lilypond
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-tangle hides /usr/share/emacs/25.2/lisp/org/ob-tangle
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-fortran hides /usr/share/emacs/25.2/lisp/org/ob-fortran
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-gnuplot hides /usr/share/emacs/25.2/lisp/org/ob-gnuplot
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-picolisp hides /usr/share/emacs/25.2/lisp/org/ob-picolisp
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-element hides /usr/share/emacs/25.2/lisp/org/org-element
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-info hides /usr/share/emacs/25.2/lisp/org/org-info
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-datetree hides /usr/share/emacs/25.2/lisp/org/org-datetree
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-dot hides /usr/share/emacs/25.2/lisp/org/ob-dot
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ox-icalendar hides /usr/share/emacs/25.2/lisp/org/ox-icalendar
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-irc hides /usr/share/emacs/25.2/lisp/org/org-irc
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-mscgen hides /usr/share/emacs/25.2/lisp/org/ob-mscgen
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-mouse hides /usr/share/emacs/25.2/lisp/org/org-mouse
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ox-beamer hides /usr/share/emacs/25.2/lisp/org/ox-beamer
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ox-org hides /usr/share/emacs/25.2/lisp/org/ox-org
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-eval hides /usr/share/emacs/25.2/lisp/org/ob-eval
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-ruby hides /usr/share/emacs/25.2/lisp/org/ob-ruby
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-awk hides /usr/share/emacs/25.2/lisp/org/ob-awk
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-lob hides /usr/share/emacs/25.2/lisp/org/ob-lob
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-maxima hides /usr/share/emacs/25.2/lisp/org/ob-maxima
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-agenda hides /usr/share/emacs/25.2/lisp/org/org-agenda
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-emacs-lisp hides /usr/share/emacs/25.2/lisp/org/ob-emacs-lisp
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ox-publish hides /usr/share/emacs/25.2/lisp/org/ox-publish
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-python hides /usr/share/emacs/25.2/lisp/org/ob-python
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ox-ascii hides /usr/share/emacs/25.2/lisp/org/ox-ascii
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-table hides /usr/share/emacs/25.2/lisp/org/org-table
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-colview hides /usr/share/emacs/25.2/lisp/org/org-colview
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-sqlite hides /usr/share/emacs/25.2/lisp/org/ob-sqlite
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ox hides /usr/share/emacs/25.2/lisp/org/ox
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-lisp hides /usr/share/emacs/25.2/lisp/org/ob-lisp
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-indent hides /usr/share/emacs/25.2/lisp/org/org-indent
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-java hides /usr/share/emacs/25.2/lisp/org/ob-java
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-footnote hides /usr/share/emacs/25.2/lisp/org/org-footnote
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-plantuml hides /usr/share/emacs/25.2/lisp/org/ob-plantuml
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-matlab hides /usr/share/emacs/25.2/lisp/org/ob-matlab
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-clojure hides /usr/share/emacs/25.2/lisp/org/ob-clojure
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-ocaml hides /usr/share/emacs/25.2/lisp/org/ob-ocaml
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-screen hides /usr/share/emacs/25.2/lisp/org/ob-screen
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-list hides /usr/share/emacs/25.2/lisp/org/org-list
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-ctags hides /usr/share/emacs/25.2/lisp/org/org-ctags
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-faces hides /usr/share/emacs/25.2/lisp/org/org-faces
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-sql hides /usr/share/emacs/25.2/lisp/org/ob-sql
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-src hides /usr/share/emacs/25.2/lisp/org/org-src
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-makefile hides /usr/share/emacs/25.2/lisp/org/ob-makefile
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-plot hides /usr/share/emacs/25.2/lisp/org/org-plot
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-R hides /usr/share/emacs/25.2/lisp/org/ob-R
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-entities hides /usr/share/emacs/25.2/lisp/org/org-entities
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-rmail hides /usr/share/emacs/25.2/lisp/org/org-rmail
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-timer hides /usr/share/emacs/25.2/lisp/org/org-timer
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-compat hides /usr/share/emacs/25.2/lisp/org/org-compat
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-js hides /usr/share/emacs/25.2/lisp/org/ob-js
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-shen hides /usr/share/emacs/25.2/lisp/org/ob-shen
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-core hides /usr/share/emacs/25.2/lisp/org/ob-core
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-C hides /usr/share/emacs/25.2/lisp/org/ob-C
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-gnus hides /usr/share/emacs/25.2/lisp/org/org-gnus
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-ditaa hides /usr/share/emacs/25.2/lisp/org/ob-ditaa
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-scala hides /usr/share/emacs/25.2/lisp/org/ob-scala
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/org-bibtex hides /usr/share/emacs/25.2/lisp/org/org-bibtex
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-table hides /usr/share/emacs/25.2/lisp/org/ob-table
/home/marek/.emacs.d/elpa/org-plus-contrib-20170807/ob-scheme hides /usr/share/emacs/25.2/lisp/org/ob-scheme
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Features:
(shadow sort mail-extr emacsbug message rfc822 mml mml-sec epg mm-decode
mm-bodies mm-encode mail-parse rfc2231 mailabbrev gmm-utils mailheader
sendmail rfc2047 rfc2045 ietf-drums mail-utils winner helm-command
cap-words superword subword smartparens-config smartparens-rust
smartparens-python smartparens-haskell smartparens paren autorevert
filenotify rainbow-delimiters aggressive-indent which-key savehist cargo
cargo-process rust-mode recentf tree-widget wid-edit python tramp-sh
helm-projectile projectile grep ibuf-ext ibuffer real-auto-save trim
helm-mode helm-config helm-easymenu async-bytecomp ace-jump-helm-line
linum avy haskell-mode haskell-cabal haskell-utils haskell-font-lock
haskell-indentation haskell-string haskell-sort-imports haskell-lexeme
haskell-align-imports haskell-compat haskell-complete-module
haskell-ghc-support noutline outline flymake etags xref project dabbrev
haskell-customize intero warnings flycheck json map find-func dash
haskell-snippets yasnippet tango-dark-theme crosshairs col-highlight
vline hl-line+ hl-line helm-company subr-x company helm-elisp helm-eval
edebug helm-files rx image-dired tramp tramp-compat tramp-loaddefs
trampver ucs-normalize shell pcomplete format-spec dired-x dired-aux
ffap thingatpt helm-buffers helm-tags helm-bookmark helm-adaptive
helm-info bookmark pp helm-locate helm-grep helm-regexp helm-external
helm-net browse-url xml url url-proxy url-privacy url-expand url-methods
url-history url-cookie url-domsuf url-util url-parse auth-source
gnus-util mm-util help-fns mail-prsvr password-cache url-vars mailcap
helm-utils compile comint ansi-color ring helm-help helm-types helm
helm-source cl-seq eieio-compat eieio eieio-core cl-macs
helm-multi-match helm-lib dired advice async edmacro kmacro use-package
diminish bind-key easy-mmode finder-inf info package epg-config seq
byte-opt gv bytecomp byte-compile cl-extra help-mode easymenu cconv
cl-loaddefs pcase cl-lib time-date mule-util tooltip eldoc electric
uniquify ediff-hook vc-hooks lisp-float-type mwheel x-win
term/common-win x-dnd tool-bar dnd fontset image regexp-opt fringe
tabulated-list newcomment elisp-mode lisp-mode prog-mode register page
menu-bar rfn-eshadow timer select scroll-bar mouse jit-lock font-lock
syntax facemenu font-core frame cl-generic cham georgian utf-8-lang
misc-lang vietnamese tibetan thai tai-viet lao korean japanese eucjp-ms
cp51932 hebrew greek romanian slovak czech european ethiopic indian
cyrillic chinese charscript case-table epa-hook jka-cmpr-hook help
simple abbrev minibuffer cl-preloaded nadvice loaddefs button faces
cus-face macroexp files text-properties overlay sha1 md5 base64 format
env code-pages mule custom widget hashtable-print-readable backquote
dbusbind inotify dynamic-setting system-font-setting font-render-setting
move-toolbar gtk x-toolkit x multi-tty make-network-process emacs)

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