Add installation scripts

doom.org

@@ -14,6 +14,50 @@
 #+property: header-args:emacs-lisp :tangle ~/.config/doom/config.el :results none :padline no
 :END:
 
+* Installation
+:PROPERTIES:
+:header-args:bash: :tangle scripts/install-emacs.sh :shebang "#!/bin/bash" :mkdirp yes
+:END:
+
+#+begin_src bash
+set -euo pipefail
+
+DOTFILES="${HOME}/.config/literate-dotfiles"
+DOOM="${HOME}/.config/emacs/bin/doom"
+#+end_src
+
+** Packages
+
+#+begin_src bash
+echo "==> Emacs packages"
+paru -S --needed emacs aspell aspell-en aspell-fr
+#+end_src
+
+** Doom Emacs
+
+#+begin_src bash
+echo "==> Installing Doom Emacs"
+git clone --depth 1 https://github.com/doomemacs/doomemacs ~/.config/emacs
+"${DOOM}" install --no-config
+#+end_src
+
+** Tangle Configuration
+
+Tangle =doom.org= to generate =config.el=, =init.el= and =packages.el=:
+
+#+begin_src bash
+echo "==> Tangling doom.org"
+emacsclient -e "(org-babel-tangle-file \"${DOTFILES}/doom.org\")" \
+    || emacs --batch -l org --eval "(org-babel-tangle-file \"${DOTFILES}/doom.org\")"
+#+end_src
+
+** Sync
+
+#+begin_src bash
+echo "==> Running doom sync"
+"${DOOM}" sync
+#+end_src
+
 * Introduction and Resources
 https://medium.com/urbint-engineering/emacs-doom-for-newbies-1f8038604e3b
 https://noelwelsh.com/posts/2019-01-10-doom-emacs.html
@@ -1273,7 +1317,7 @@ https://kitchingroup.cheme.cmu.edu/blog/2016/11/07/Better-equation-numbering-in-
           (counter -1)
           (numberp))
 
-      (setq results (loop for (begin .  env) in
+      (setq results (cl-loop for (begin .  env) in
                           (org-element-map (org-element-parse-buffer) 'latex-environment
                             (lambda (env)
                               (cons
@@ -1283,20 +1327,20 @@ https://kitchingroup.cheme.cmu.edu/blog/2016/11/07/Better-equation-numbering-in-
                           (cond
                            ((and (string-match "\\\\begin{equation}" env)
                                  (not (string-match "\\\\tag{" env)))
-                            (incf counter)
+                            (cl-incf counter)
                             (cons begin counter))
                            ((string-match "\\\\begin{align}" env)
                             (prog2
-                                (incf counter)
+                                (cl-incf counter)
                                 (cons begin counter)
                               (with-temp-buffer
                                 (insert env)
                                 (goto-char (point-min))
                                 ;; \\ is used for a new line. Each one leads to a number
-                                (incf counter (count-matches "\\\\$"))
+                                (cl-incf counter (count-matches "\\\\$"))
                                 ;; unless there are nonumbers.
                                 (goto-char (point-min))
-                                (decf counter (count-matches "\\nonumber")))))
+                                (cl-decf counter (count-matches "\\nonumber")))))
                            (t
                             (cons begin nil)))))
 
@@ -3019,12 +3063,38 @@ Provides nice functions such as:
   )
 #+end_src
 
+* Claude Code
+#+begin_src emacs-lisp
+(use-package! agent-shell
+  :config
+  (setq agent-shell-anthropic-authentication
+      (agent-shell-anthropic-make-authentication :login t))
+
+  (setq agent-shell-preferred-agent-config (agent-shell-anthropic-make-claude-code-config))
+  ;; Evil state-specific RET behavior: insert mode = newline, normal mode = send
+  (evil-define-key 'insert agent-shell-mode-map (kbd "M-RET") #'newline)
+  (evil-define-key 'insert agent-shell-mode-map (kbd "RET") #'comint-send-input)
+  (evil-define-key 'normal agent-shell-mode-map (kbd "RET") #'comint-send-input)
+  ;; n and p are bound in agent-shell-mode-map; restore self-insert in insert mode
+  (evil-define-key 'insert agent-shell-mode-map (kbd "n") #'self-insert-command)
+  (evil-define-key 'insert agent-shell-mode-map (kbd "p") #'self-insert-command)
+  
+  (evil-define-key 'normal agent-shell-diff-mode-map (kbd "C-c C-o") #'agent-shell-diff-open-file)
+  (evil-define-key 'normal agent-shell-diff-mode-map (kbd "C-c C-a") #'agent-shell-diff-accept-all)
+
+  ;; Configure *agent-shell-diff* buffers to start in Emacs state
+  (add-hook 'diff-mode-hook
+	    (lambda ()
+	      (when (string-match-p "\\*agent-shell-diff\\*" (buffer-name))
+		(evil-emacs-state)))))
+#+end_src
+
 * Doom =init.el=
 #+begin_src emacs-lisp :tangle ~/.config/doom/init.el
 (doom! :completion
        company           ; the ultimate code completion backend
        (corfu +orderless)  ; complete with cap(f), cape and a flying feather!
-       helm              ; the *other* search engine for love and life
+       ;;helm              ; the *other* search engine for love and life
        ;;ido               ; the other *other* search engine...
        ;;ivy               ; a search engine for love and life
        vertico           ; the search engine of the future
@@ -3209,6 +3279,8 @@ https://github.com/doomemacs/doomemacs/issues/6478
 #+begin_src emacs-lisp
 ;; Org-mode modules for citations, cross-references, bibliographies
 (package! org-ref)
+;; helm-bibtex (declared explicitly since the helm Doom module is not used)
+(package! helm-bibtex)
 #+end_src
 
 #+begin_src emacs-lisp
@@ -3261,6 +3333,13 @@ https://github.com/doomemacs/doomemacs/issues/6478
            :files ("resources" "*.el")))
 #+end_src
 
+** Claude Code
+#+begin_src emacs-lisp
+(package! shell-maker)
+(package! acp)
+(package! agent-shell)
+#+end_src
+
 ** Not used anymore :noexport:
 :PROPERTIES:
 :header-args:emacs-lisp: :tangle no