Emacs Config

(setq custom-file (locate-user-emacs-file "custom.el"))
;; create custom.el if it does not exists.
(unless (file-exists-p custom-file)
  (write-region "" nil custom-file))
(load custom-file)

;; package
(setq package-enable-at-startup nil)
;; (defvar bootstrap-version)
;; (let ((bootstrap-file
;;        (expand-file-name "straight/repos/straight.el/bootstrap.el" user-emacs-directory))
;;       (bootstrap-version 6))
;;   (unless (file-exists-p bootstrap-file)
;;     (with-current-buffer
;;         (url-retrieve-synchronously
;;          "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el"
;;          'silent 'inhibit-cookies)
;;       (goto-char (point-max))
;;       (eval-print-last-sexp)))
;;   (load bootstrap-file nil 'nomessage))

;; (straight-use-package 'use-package)

;; MELPA package
(require 'package)
(add-to-list 'package-archives '("melpa" . "https://melpa.org/packages/") t)
;; (setq package-archives '(("melpa" . "https://melpa.org/packages/")))
(package-initialize)

;; Install 'use-package if not installed.
(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))

;; For use-package keywords:
;; https://jwiegley.github.io/use-package/keywords/
(eval-when-compile (require 'use-package))

;; Ensure for all packages
(require 'use-package-ensure)
(setq use-package-always-ensure t)

;; Increase the garbage collection threshold to 100MB to reduced startup time.
;; See https://www.reddit.com/r/emacs/comments/3kqt6e
(setq gc-cons-threshold (* 1024 1024 100))

;; Turn off mouse interface early in startup to avoid momentary display.
(menu-bar-mode -1)

(tooltip-mode -1)

;; On Emacs without X, tool-bar-mode and scroll-bar-mode are not defined.
(when (fboundp 'tool-bar-mode)
  (tool-bar-mode -1))
(when (fboundp 'scroll-bar-mode)
  (scroll-bar-mode -1))

;; Show column number in the mode line.
(column-number-mode)

;; Inhibit the startup screen and shorten the scratch buffer's message.
(setq inhibit-startup-screen t)
(setq initial-scratch-message ";; scratch buffer\n\n")

(use-package hydra
  :commands defhydra
  :init
  (defhydra hydra-file-menu (:hint nil
                                   :foreign-keys warn
                                   :exit t
                                   :pre (setq which-key-inhibit t)
                                   :post (setq which-key-inhibit nil))
    "
^Emacs^             Org              ^Blog^
^-----^------------------------------------------------
_er_: reload        i: inbox.org     _bb_: drafts.org
_ed_: dotemacs.org  t: task.org      _bp_: posts.org
_ep_: private.org   d: diary.org
_el_: local.org     n: note.org
"
    ("er" (load-file user-init-file))
    ("ed" (let ((vc-follow-symlinks t)) (find-file (locate-user-emacs-file "dotemacs.org"))))
    ("ep" (let ((vc-follow-symlinks t)) (find-file (locate-user-emacs-file "private.org"))))
    ("el" (let ((vc-follow-symlinks t)) (find-file (locate-user-emacs-file (concat "local-" (system-name) ".org")))))
    ("i" (find-file (expand-file-name "inbox.org" org-directory)))
    ("t" (find-file (expand-file-name "task.org" org-directory)))
    ("d" (find-file (expand-file-name "diary.org" org-directory)))
    ("n" (find-file (expand-file-name "note.org" org-directory)))
    ("bb" (find-file (expand-file-name "drafts.org" org-directory)))
    ("bp" (find-file "~/sync/blog/org-content/posts.org"))
    ("q" nil "quit menu" :color blue))
  (global-set-key (kbd "C-c e") 'hydra-file-menu/body))

;; Don't forget to handle minibuffer with "minibuffer-keyboard-quit".
(global-set-key (kbd "<escape>") 'keyboard-quit)

;; Avoid entering the ~repeat-complex-cammand~ when quiting everything with ~C-x~.
(global-unset-key (kbd "C-x <escape> <escape>")) ; repeat-complex-command

;; Save backup files to a dedicated directory.
(setq backup-directory-alist '(("." . "~/.emacs.d/backups")))
(setq delete-old-versions -1)

;; Make numeric backup versions unconditionally.
(setq version-control t)
(setq vc-make-backup-files t)
(setq auto-save-file-name-transforms '((".*" "~/.emacs.d/auto-save-list/" t)))

;; Do not create lock files.
(setq create-lockfiles nil)

(setq native-comp-async-report-warnings-errors nil)

(use-package org-auto-tangle
  :defer t
  :hook (org-mode . org-auto-tangle-mode))

;; Use year/month/day
(setq calendar-date-style 'iso)

(xterm-mouse-mode +1)

;; Remember and restore the last cursor location of opened files
(save-place-mode 1)

;; Don't pop up UI dialogs when prompting
(setq use-dialog-box nil)

;; Disable the alarm bell (https://www.emacswiki.org/emacs/AlarmBell).
(setq ring-bell-function 'ignore)

;; Use shorter "y" or "n" to confirm killing emacs.
(setq confirm-kill-emacs 'y-or-n-p)

;; Disabe some Emacs's default keybindings.
(global-unset-key (kbd "C-v"))  ; scroll-up-command
(global-unset-key (kbd "M-v"))  ; scroll-down-command
(global-unset-key (kbd "C-n"))  ; next line
(global-unset-key (kbd "C-p"))  ; previous line
(global-unset-key (kbd "C-b"))  ; previous char
;; (global-unset-key (kbd "C-f"))  ; next char
(global-unset-key (kbd "C-t"))  ; switch char
(global-unset-key (kbd "C-l"))  ; recenter
(global-unset-key (kbd "C-j"))  ; (electric-newline-and-maybe-indent)
(global-unset-key (kbd "M-l"))  ; downcase-word
(global-unset-key (kbd "M-u"))  ; upcase-wrod

;; Disable the "numeric argument". When used, I use the =C-u= prefix.
(dolist (prefix '("M-" "C-M-"))
  (global-unset-key (kbd (concat prefix "-")))
  (dotimes (i 10)
    (global-unset-key (kbd (concat prefix (number-to-string i))))))

(defun my/edit-mode ()
  (visual-line-mode +1)               ; enable "word-wrap"
  (toggle-truncate-lines -1)
  ;; (hl-line-mode +1)
  (local-set-key (kbd "C-S-s") 'write-file)
  (setq cursor-type 'bar)
  (setq show-trailing-whitespace t))

(defun my/text-mode ()
  (my/edit-mode)
  (goto-address-mode +1)
  (flyspell-mode))

(defun my/prog-mode ()
  (display-line-numbers-mode +1)
  (my/edit-mode)
  (show-paren-mode +1)
  (goto-address-prog-mode +1)
  (flyspell-prog-mode))

(add-hook 'text-mode-hook 'my/text-mode)
(add-hook 'prog-mode-hook 'my/prog-mode)
(add-hook 'conf-mode-hook 'my/prog-mode)

;; Removes the overlay properties which flyspell uses on incorrect words for mouse operations.
;; https://emacs.stackexchange.com/a/55708
(defun make-flyspell-overlay-return-mouse-stuff (overlay)
  (overlay-put overlay 'help-echo nil)
  (overlay-put overlay 'keymap nil)
  (overlay-put overlay 'mouse-face nil))
(advice-add 'make-flyspell-overlay :filter-return #'make-flyspell-overlay-return-mouse-stuff)

;; Remove trailing whitespace except current line.
;; https://stackoverflow.com/a/35781486/1747877
(defun my/delete-trailing-whitespace-except-current-line ()
  "Delete trailing whitespace in the whole buffer, except on the current line.
  The current line exception is because we do want to remove any whitespace
  on the current line on saving the file (`before-save-hook') while we are
  in-between typing something.

  Do not do anything if `do-not-delete-trailing-whitespace' is non-nil."
  (interactive)
  (when (not (bound-and-true-p do-not-delete-trailing-whitespace))
    (delete-trailing-whitespace (point-min) (line-beginning-position))
    (delete-trailing-whitespace (line-end-position) (point-max))))

(add-hook 'before-save-hook #'my/delete-trailing-whitespace-except-current-line)

(defun my/save-buffer (&optional arg)
  "Like `save-buffer', but does nothing if buffer is not visiting a file."
  (interactive "p")
  (unless (or (buffer-file-name)                       ; regular buffer
              (buffer-file-name (buffer-base-buffer))) ; indirect buffer
    (user-error "Use 'M-x save-buffer' to save this buffer."))
  (progn
    (my/delete-trailing-whitespace-except-current-line)
    (save-buffer arg)))

(global-set-key [remap save-buffer] #'my/save-buffer)

;; Auto save buffer if idled for 2 seconds.
(setq auto-save-timeout 2)
(auto-save-visited-mode 1)

;; Watch and reload the file changed on the disk.
(setq auto-revert-remote-files t)
(global-auto-revert-mode 1)

;; Use a timer instead of file notification.
;;
;; File notification does not work well on Emacs 29.1.2.
;; Error: "file-notify--call-handler: Symbol’s function definition is void: nil"
(setq auto-revert-use-notify nil
      auto-revert-interval 5)

;; Delete the selected text first before editing.
(delete-selection-mode +1)

;; Mouse middle-click yanks where the point is, not where the mouse is.
(setq mouse-yank-at-point t)

(if (fboundp 'pixel-scroll-precision-mode)
    (pixel-scroll-precision-mode 1)
  ;; Smooth Scrolling: https://www.emacswiki.org/emacs/SmoothScrolling
  (setq scroll-conservatively 10000
        scroll-step 1))

;; move line up
(defun my/move-line-up ()
  (interactive)
  (transpose-lines 1)
  (previous-line 2))
(global-set-key [(meta shift up)] 'my/move-line-up)

;; move line down
(defun my/move-line-down ()
  (interactive)
  (next-line 1)
  (transpose-lines 1)
  (previous-line 1))

(global-set-key [(meta shift down)] 'my/move-line-down)

(setq sentence-end-double-space nil)

(setq-default indent-tabs-mode nil)

;; rename-visited-file is introduced in Emacs 29.
(unless (fboundp 'rename-visited-file)
  (defun rename-visited-file ()
    "Renames the current buffer and the file it is visiting."
    (interactive)
    (let ((name (buffer-name))
          (filename (buffer-file-name)))
      (if (not (and filename (file-exists-p filename)))
          (error "Buffer '%s' is not visiting a file!" name)
        (let ((new-name (read-file-name "New name: " filename)))
          (if (get-buffer new-name)
              (error "A buffer named '%s' already exists!" new-name)
            (rename-file filename new-name 1)
            (rename-buffer new-name)
            (set-visited-file-name new-name)
            (set-buffer-modified-p nil)
            (message "File '%s' successfully renamed to '%s'"
                     name (file-name-nondirectory new-name))))))))

(global-set-key (kbd "C-x R") 'rename-visited-file)

(defun my/delete-file-and-buffer ()
  "Kills the current buffer and deletes the file it is visiting."
  (interactive)
  (let ((filename (buffer-file-name)))
    (if filename
        (if (y-or-n-p (concat "Do you really want to delete file " filename " ?"))
            (progn
              (delete-file filename)
              (message "Deleted file %s." filename)
              (kill-buffer)))
      (message "Not a file visiting buffer!"))))

(global-set-key (kbd "C-x K") 'my/delete-file-and-buffer)

(defun my/sudo-find-file (file-name)
  "Like find file, but opens the file as root."
  (interactive "FSudo Find File: ")
  (let ((tramp-file-name (concat "/sudo::" (expand-file-name file-name))))
    (find-file tramp-file-name)))

(defun my/insert-current-date () (interactive)
       (insert (shell-command-to-string "echo -n $(date +%Y-%m-%d)")))

(defhydra my/hydra-snippets (:hint nil
                             :foreign-keys warn
                             :exit t)
  "Snippets"
  ("d" (my/insert-current-date) "Current Date (yyyy-mm-dd)")
  ("q" nil "Quit Menu"))

(global-set-key (kbd "C-c s") 'my/hydra-snippets/body)

;; for Emacs 28 or above
(setq tramp-verbose 2)
;; for Emacs 27 or below
(setq tramp-message-show-message nil)

(defun with-case-fold-search (orig-fun &rest args)
  (let ((case-fold-search nil))
    (apply orig-fun args)))

(advice-add 'replace-string :around #'with-case-fold-search)

(use-package modus-themes
  :init
  (setq modus-themes-to-toggle '(modus-operandi modus-vivendi-tinted))
  (setq modus-themes-org-blocks 'gray-background)
  (setq modus-themes-headings
        '((agenda-date . (1.2))))

  (setq modus-themes-common-palette-overrides
        '((fg-heading-1 blue-cooler)
          (fg-heading-2 blue)
          (fg-heading-3 blue-warmer)))
  (load-theme 'modus-vivendi-tinted :no-confirm)
  :bind ("<f5>" . modus-themes-toggle))

;; https://github.com/seagle0128/doom-modeline
(use-package doom-modeline
  :init
  (doom-modeline-mode +1))

;; Doom modeline needs all-the-icons.
(use-package all-the-icons)

(use-package winner
  :init
  (winner-mode +1))

(use-package windmove
  :bind
  ("M-s-<up>" . 'windmove-up)
  ("M-s-<down>" . 'windmove-down)
  ("M-s-<left>" . 'windmove-left)
  ("M-s-<right>" . 'windmove-right))

(use-package ace-window
  :bind
  ("M-o" . 'ace-window)
  :custom
  (aw-keys '(?a ?s ?d ?f ?g ?h ?j ?k ?l))
  (aw-scope 'frame))

(defun my/toggle-current-window-dedication ()
  (interactive)
  (let* ((window (selected-window))
         (dedicated (window-dedicated-p window)))
    (set-window-dedicated-p window (not dedicated))
    (message "Window %sdedicated to %s"
             (if dedicated "no longer " "")
             (buffer-name))))
(global-set-key (kbd "<f11>") 'my/toggle-current-window-dedication)

(global-set-key (kbd "C-x 2")
                (lambda ()
                  (interactive)
                  (split-window-vertically)
                  (other-window 1)))
(global-set-key (kbd "C-x 3")
                (lambda ()
                  (interactive)
                  (split-window-horizontally)
                  (other-window 1)))

(use-package emacs
  :config
  (setq tab-bar-close-button-show nil)
  (setq tab-bar-new-button-show nil)

  ;; hide the tab bar when only one tab. Looks better especially when editting a file with emacsclient.
  (setq tab-bar-show 1)
  ;; Show the absolute number of the tab
  (setq tab-bar-tab-hints t)
  ;; Switch to tab by C-?
  (setq tab-bar-select-tab-modifiers '(control))

  (tab-bar-mode +1)
  :bind
  ("C-<tab>" . tab-next))

(use-package vertico
  :init
  (vertico-mode)
  (setq vertico-count 25)
  :bind
  (:map vertico-map
        ([escape] . minibuffer-keyboard-quit)
        ("<prior>" . vertico-scroll-down)
        ("<next>" . vertico-scroll-up)))

;; Persist history over Emacs restarts. Vertico sorts by history position.
(use-package savehist
  :init
  (savehist-mode))

;; A few more useful configurations...
(use-package emacs
  :init
  ;; Add prompt indicator to `completing-read-multiple'.
  ;; We display [CRM<separator>], e.g., [CRM,] if the separator is a comma.
  (defun crm-indicator (args)
    (cons (format "[CRM%s] %s"
                  (replace-regexp-in-string
                   "\\`\\[.*?]\\*\\|\\[.*?]\\*\\'" ""
                   crm-separator)
                  (car args))
          (cdr args)))
  (advice-add #'completing-read-multiple :filter-args #'crm-indicator)

  ;; Do not allow the cursor in the minibuffer prompt
  (setq minibuffer-prompt-properties
        '(read-only t cursor-intangible t face minibuffer-prompt))
  (add-hook 'minibuffer-setup-hook #'cursor-intangible-mode)

  ;; Emacs 28: Hide commands in M-x which do not work in the current mode.
  ;; Vertico commands are hidden in normal buffers.
  (setq read-extended-command-predicate
        #'command-completion-default-include-p)

  ;; Enable recursive minibuffers
  (setq enable-recursive-minibuffers t))

;; Optionally use the `orderless' completion style.
(use-package orderless
  :init
  ;; Configure a custom style dispatcher (see the Consult wiki)
  ;; (setq orderless-style-dispatchers '(+orderless-dispatch)
  ;;       orderless-component-separator #'orderless-escapable-split-on-space)
  (setq completion-styles '(orderless basic)
        completion-category-defaults nil
        completion-category-overrides '((file (styles partial-completion)))))

(use-package consult
  :bind
  ;; ("C-f" . consult-line)
  ("C-s" . consult-line)
  ("C-b" . consult-bookmark)
  ("C-j" . consult-imenu)
  :init
  (with-eval-after-load "org"
    (define-key org-mode-map (kbd "C-j") #'consult-org-heading)))

(use-package marginalia
  :init
  (setq marginalia-align 'center)
  (marginalia-mode))

(use-package embark
  :bind
  (("C-." . embark-act)         ;; pick some comfortable binding
   ("C-;" . embark-dwim)        ;; good alternative: M-.
   ("C-h B" . embark-bindings)) ;; alternative for "describe-bindings"

  :init
  ;; Optionally replace the key help with a completing-read interface
  (setq prefix-help-command #'embark-prefix-help-command)

  :config
  ;; Hide the mode line of the Embark live/completions buffers
  (add-to-list 'display-buffer-alist
               '("\\`\\*Embark Collect \\(Live\\|Completions\\)\\*"
                 nil
                 (window-parameters (mode-line-format . none)))))

;; Consult users will also want the embark-consult package.
(use-package embark-consult
  :hook
  (embark-collect-mode . consult-preview-at-point-mode))

;; Hydra menu to for consult.
(defhydra hydra-consult-menu (:hint nil
                              :foreign-keys warn
                              :exit t
                              :pre (setq which-key-inhibit t)
                              :post (setq which-key-inhibit nil))
  "===== Consult Menu (F12) =====\n"
  ("f" (my/consult-org-agenda) "Agenda")
  ("r" (consult-recent-file) "Recentf")
  ("q" nil "quit menu" :color blue))
(global-set-key (kbd "<f8>") 'hydra-consult-menu/body)

(use-package which-key
  :custom
  ; (which-key-idle-delay 10000 "Set idle delay to infinite so it never trigger automatically")
  ; (which-key-show-early-on-C-h t "Allow C-h to trigger which-key before it is done automatically.")
  ; (which-key-idle-secondary-delay 0.05)
  (which-key-mode +1 "Non-nil if which-Key mode is enabled"))

;; Adding a "/" so that =find-file= finds the files under =~/org/=.
(setq org-directory "~/org/")

(defun my/expand-org-file-name (filename)
  (expand-file-name filename org-directory))

(setq my/org-inbox-file (my/expand-org-file-name "inbox.org")
      my/org-task-file (my/expand-org-file-name "task.org")
      my/org-task-archive-file (my/expand-org-file-name "task.org_archive")
      my/org-note-file (my/expand-org-file-name "note.org")
      my/org-checklist-file (my/expand-org-file-name "checklist.org")
      my/org-review-file (my/expand-org-file-name "review.org")
      my/org-vocab-file (my/expand-org-file-name "drill/vocab.org")
      my/org-calendar-directory (my/expand-org-file-name ".calendar")
      my/org-attachment-directory (my/expand-org-file-name ".attachment"))

(use-package org
  :bind
  (:map org-mode-map ("C-x n n" . org-toggle-narrow-to-subtree))
  :config

  ;; Enable the =org-indent-mode= by default.
  (setq org-startup-indented t)

  ;; Reduce org-indent-indentation-per-level from 2 to 1.
  ;;
  ;; This keeps =org-tags-column= the same for all headings.
  (setq org-indent-indentation-per-level 1)

  :hook
  ;; Reserve "C-c <arrow>" for windmove
  (org-mode . (lambda ()
                (local-unset-key (kbd "C-c <left>"))
                (local-unset-key (kbd "C-c <right>"))
                (local-unset-key (kbd "C-c <up>"))
                (local-unset-key (kbd "C-c <down>")))))

(global-set-key (kbd "C-c c") 'org-capture)

;; The default file for capturing.
(setq org-default-notes-file my/org-inbox-file)

;; Org Capture Templates
;;
;; See https://orgmode.org/manual/Template-elements.html#index-org_002ddefault_002dnotes_002dfile-1
(setq org-capture-templates nil)
(add-to-list
 'org-capture-templates
 '("i" "Inbox" entry (file org-default-notes-file)
   "* %?\n%i\n%a"))

(add-to-list
 'org-capture-templates
 '("p" "Project" entry (file+headline my/org-task-file "Projects")
   (file "~/org/.template/project.org")))

(add-to-list
 'org-capture-templates
 '("d" "Review: Daily Review" entry (file+olp+datetree my/org-review-file)
   (file "~/org/.template/review-daily.org")
   :tree-type week :clock-in t :clock-keep t :immediate-finish t :jump-to-captured t))

(add-to-list
 'org-capture-templates
 '("w" "Review: Weekly Review" entry (file+datetree my/org-review-file)
   (file "~/org/.template/review-weekly.org")
   :clock-in t :clock-keep t :immediate-finish t :jump-to-captured t))

(add-to-list
 'org-capture-templates
 '("v" "Vocab" entry (file+headline my/org-vocab-file "Translation")
   "* %? :drill:\n\n** Translation\n\n** Definition\n"))

(use-package org-cliplink)

(require 'org-attach)
(setq org-attach-id-dir my/org-attachment-directory)
(setq org-attach-use-inheritance t)

;; Use timestamp as ID and attachment folder. See https://helpdeskheadesk.net/2022-03-13/
;; (setq org-id-method 'ts)
;; (setq org-attach-id-to-path-function-list
;;       '(org-attach-id-ts-folder-format
;;         org-attach-id-uuid-folder-format))
;; Shorten the Org timestamp ID
;; (setq org-id-ts-format "%Y%m%dT%H%M%S")

;; Sets default-directory to org-directory so that =M-x magit= from the agenda view does not ask me for a dir.
(global-set-key (kbd "C-c a")
                (lambda ()
                  (interactive)
                  (let ((default-directory org-directory)) (org-agenda))))

;; My agenda files.
(setq org-agenda-files (list my/org-inbox-file my/org-task-file my/org-calendar-directory))

;; Trying to use the current window as agenda frame.
(setq org-agenda-window-setup 'current-window)

;; Use sticky agenda since I need different agenda views (personal and work) at the same time.
(setq org-agenda-sticky t)

;; Just today
(setq org-agenda-span 'day)

;; Hide all scheduled todo.
(setq org-agenda-todo-ignore-scheduled 'all)

;; Ignores "far" deadline TODO items from TODO list.
(setq org-agenda-todo-ignore-deadlines 'far)

;; Hide all scheduled todo, from tags search view, like tags-todo.
(setq org-agenda-tags-todo-honor-ignore-options t)

;; Hide all done todo in agenda
(setq org-agenda-skip-scheduled-if-done t)

;; Hide task until the scheduled date.
(setq org-agenda-skip-deadline-prewarning-if-scheduled 'pre-scheduled)


;; Use an indirect buffer after <Tab> (org-agenda-goto) or <Enter> (org-agenda-switch-to).
;;
;; Also see https://emacs.stackexchange.com/a/17822
;; (advice-add 'org-agenda-goto :after
;;             (lambda (&rest args)
;;               (org-tree-to-indirect-buffer)))
;; (advice-add 'org-agenda-switch-to :after
;;             (lambda (&rest args)
;;               (org-tree-to-indirect-buffer)))

;; Narrow to subtree after <Tab> (org-agenda-goto) or <Enter> (org-agenda-switch-to).
;; (advice-add 'org-agenda-goto :after
;;             (lambda (&rest args)
;;               (org-narrow-to-subtree)))
;; (advice-add 'org-agenda-switch-to :after
;;             (lambda (&rest args)
;;               (org-narrow-to-subtree)))

(defun my/consult-org-agenda ()
  (interactive)
  (consult-org-agenda)
  (org-tree-to-indirect-buffer))

(defun my/consult-org-task-and-note ()
  (interactive)
  (consult-org-heading
   nil
   (list my/org-inbox-file my/org-task-file my/org-task-archive-file my/org-note-file my/org-checklist-file)))

(defun my/consult-org-note ()
  (interactive)
  (consult-org-heading nil (list my/org-task-file my/org-task-archive-file my/org-note-file)))

(global-set-key (kbd "M-J") #'my/consult-org-task-and-note)
(global-set-key (kbd "<f1>") #'my/consult-org-task-and-note)
(global-set-key (kbd "<f2>") #'my/consult-org-note)

(defun my/consult-ripgrep-org-directory ()
  (interactive)
  ;; Add "--no-ignore-vcs" to the rg command so todo.org could be searched.
  (let ((consult-ripgrep-args
         "rg --null --line-buffered --color=never --max-columns=1000 --path-separator /   --smart-case --no-heading --line-number --no-ignore-vcs ."))
    (consult-ripgrep org-directory "")))

(if (eq system-type 'darwin)
    (global-set-key (kbd "s-F") 'my/consult-ripgrep-org-directory)
    (global-set-key (kbd "C-S-f") 'my/consult-ripgrep-org-directory))

;; Include the file name into the path in refile target.
(setq org-refile-use-outline-path 'file)
(setq org-outline-path-complete-in-steps nil)
(setq org-refile-targets
      '((nil :maxlevel . 2)
        (my/org-task-file :maxlevel . 3)))

(setq org-enforce-todo-dependencies t)
(setq org-log-into-drawer t)

;; 4 priorities: A, B, C, D (default)
(setq org-priority-default 68
      org-priority-lowest 68)

;; Interstitial Journaling: add note to CLOCK entry after clocking out
;; https://emacs.stackexchange.com/questions/37526/add-note-to-clock-entry-after-clocking-out
(setq org-log-note-clock-out t)

(defun my/sync-calendar()
  (interactive)
  (message "Synchronizing...")
  (shell-command "~/org/.calendar/fetch.sh")
  (message "Synchronized."))

(defun ndk/heading-title ()
  "Get the heading title."
  (save-excursion
    (if (not (org-at-heading-p))
        (org-previous-visible-heading 1))
    (org-element-property :title (org-element-at-point))))

(defun ndk/org-breadcrumbs ()
  "Get the chain of headings from the top level down
    to the current heading."
  (let ((breadcrumbs (org-format-outline-path
                      (org-get-outline-path)
                      (1- (frame-width))
                      nil " > "))
        (title (ndk/heading-title)))
    (if (string-empty-p breadcrumbs)
        title
      (format "%s" breadcrumbs))))

(defun ndk/set-header-line-format()
  (setq header-line-format '(:eval (ndk/org-breadcrumbs))))

(add-hook 'org-mode-hook #'ndk/set-header-line-format)

(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp . t) (shell . t)))

(setq org-insert-heading-respect-content t)

(setq org-clock-mode-line-total 'current)
(setq org-show-notification-timeout 3600)

(org-clock-auto-clockout-insinuate)

;; Create an indirect buffer for the current clocking task, and focus into it.
(defun my/org-clock-goto ()
  (interactive)
  (org-clock-goto)
  (org-tree-to-indirect-buffer)
  (other-window 1)
  (delete-other-windows))
(global-set-key (kbd "C-c C-x j") 'my/org-clock-goto)

(setq org-startup-with-inline-images t)

;; allows overriding the image width
(setq org-image-actual-width nil)

(defun my/denote-random-note (&optional directory)
  "Open a random denote."
  (interactive)
  (let* ((denote-directory (or directory denote-directory))
         (files (denote-directory-files)))
    (find-file (nth (random (length files)) files))))

(defun my/project-org-file-file ()
  (interactive)
  (let ((default-directory org-directory)) (project-find-file)))

(use-package denote
  :bind
  ("C-c n n" . 'denote)
  ;; ("C-c n f" . 'denote-open-or-create)
  ("C-c n f" . 'my/project-org-file-file)
  ("C-c n k" . 'denote-keywords-add)    ;; update file name automatically
  ("C-c n K" . 'denote-keywords-remove) ;; update file name automatically
  ("C-c n u" . 'denote-rename-file-using-front-matter)
  ("C-c n l" . 'denote-link-find-backlink)
  ("C-c n r" . 'my/denote-random-note)
  :init
  (setq denote-directory (expand-file-name org-directory))
  :config
  (setq denote-known-keywords '("emacs"))
  (setq denote-prompts '(subdirectory title))
  (setq denote-excluded-directories-regexp ".attachment")

  ;; Makes the denote links different from usual link.
  (set-face-attribute 'denote-faces-link
                      nil :foreground "magenta" :inherit 'link)

  ;; Remove the date and the identifier. They are duplicated with the file name.
  ;; I want to remove filetags too but denote-keyword-* need that.
  (setq denote-org-front-matter "#+title: %1$s\n#+filetags: %3$s\n")

  (add-hook 'dired-mode-hook #'denote-dired-mode))

;; allow empty keyword
(defun denote-rename-file-using-front-matter (file &optional auto-confirm)
  (interactive (list (buffer-file-name) current-prefix-arg))
  (when (buffer-modified-p)
    (if (or auto-confirm
            (y-or-n-p "Would you like to save the buffer?"))
        (save-buffer)
      (user-error "Save buffer before proceeding")))
  (unless (denote-file-is-writable-and-supported-p file)
    (user-error "The file is not writable or does not have a supported file extension"))
  (if-let* ((file-type (denote-filetype-heuristics file))
            (title (denote-retrieve-title-value file file-type))
            (extension (file-name-extension file t))
            (id (denote-retrieve-or-create-file-identifier file))
            (dir (file-name-directory file))
            (new-name (denote-format-file-name
                       dir id (denote-retrieve-keywords-value file file-type) (denote-sluggify title) extension)))
      (when (or auto-confirm
                (denote-rename-file-prompt file new-name))
        (denote-rename-file-and-buffer file new-name)
        (denote-update-dired-buffers))
    (user-error "No front matter for title and/or keywords")))

;; (use-package consult-denote
;;   :straight (consult-denote :type git :host codeberg :repo "whhone/consult-denote")
;;   :after denote
;;   :bind
;;   ("C-c n i" . 'consult-denote-link-insert-link)
;;   ("C-c n f" . 'consult-denote-open-or-create)
;;   ("C-c n F" . 'consult-denote-ripgrep))

(use-package ox-hugo
  :after ox)

;; Do not export with TOC, e.g., with org-md-export-as-markdown, org-ascii-export-as-ascii
(setq org-export-with-toc nil)

;; (setq org-export-with-section-numbers nil)

;; https://orgmode.org/worg/org-contrib/org-drill.html
(use-package org-drill
  :custom
  (org-drill-save-buffers-after-drill-sessions-p nil "Save buffers after drill sessions without prompt.")
  (org-drill-maximum-items-per-session 10 "Reduce from the default 30 to make it to become a habit.")
  :bind
  ("C-c d" . org-drill))

;; https://github.com/xuchunyang/youdao-dictionary.el
(use-package youdao-dictionary
  :config
  (setq url-automatic-caching t) ; enable cache
  :bind
  ("C-c v" . youdao-dictionary-search-at-point+)
  ("C-c V" . youdao-dictionary-play-voice-at-point))

(defun my/browse-dictionary-at-point ()
  (interactive)
  (browse-url (concat "https://dictionary.cambridge.org/zht/詞典/英語-漢語-繁體/" (thing-at-point 'word))))

(use-package google-translate
  :config
  (setq google-translate-output-destination 'popup)
  (setq google-translate-default-source-language "en")
  (setq google-translate-default-target-language "zh-TW")
  :bind
  ("C-c b" . google-translate-at-point))

;; https://www.powerthesaurus.org/
(use-package powerthesaurus
  :bind
  ("M-`" . powerthesaurus-lookup-word-dwim))

(use-package writegood-mode
  :config
  (setq writegood-weasel-words
        '("very" "rather" "really" "quite" "in fact" "just" "so" "pretty" "of course" "surely" "that said" "actually")))

(use-package magit)

(use-package diff-hl
  :init
  (global-diff-hl-mode)
  :hook
  (magit-pre-refresh . diff-hl-magit-pre-refresh)
  (magit-post-refresh . diff-hl-magit-post-refresh))

(use-package vterm
  :config
  (define-key vterm-mode-map (kbd "<f1>") nil)
  (define-key vterm-mode-map (kbd "<f2>") nil)
  (define-key vterm-mode-map (kbd "<f3>") nil)
  (define-key vterm-mode-map (kbd "<f4>") nil)
  (define-key vterm-mode-map (kbd "<f5>") nil)
  (define-key vterm-mode-map (kbd "<f6>") nil)
  (define-key vterm-mode-map (kbd "<f7>") nil)
  (define-key vterm-mode-map (kbd "<f8>") nil)
  (define-key vterm-mode-map (kbd "<f9>") nil)
  (define-key vterm-mode-map (kbd "<f10>") nil)
  (define-key vterm-mode-map (kbd "<f11>") nil)
  (define-key vterm-mode-map (kbd "<f12>") nil)

  (setq vterm-shell "zsh")
  (setq vterm-tramp-shells '(("docker" "/bin/sh") ("ssh" "/bin/zsh")))
  :hook
  (vterm-mode . goto-address-mode))

(use-package vterm-toggle
  :config
  ;; show vterm buffer in side window
  (add-to-list 'display-buffer-alist
               '("\\*vterm\\*"
                 (display-buffer-reuse-window display-buffer-in-side-window)
                 (side . bottom)
                 (dedicated . t)
                 (reusable-frames . visible) ;; depends on how I use Emacs / Emacs Client
                 (window-height . 0.5)))
  :bind
  ("s-<return>" . vterm-toggle)
  ("C-`" . vterm-toggle)
  ("C-c t" . vterm-toggle))

(add-hook 'after-save-hook
          'executable-make-buffer-file-executable-if-script-p)

(use-package yaml-mode)

(use-package web-mode
  :init
  (add-to-list 'auto-mode-alist '("\\.html\\'" . web-mode))

  ;; TODO: Use .dir.local because not all .html are go template
  (setq web-mode-engines-alist
    '(("go" . "\\.html\\'"))))

(use-package markdown-mode
  :bind
  (:map markdown-mode-map ("M-<left>" . markdown-promote))
  (:map markdown-mode-map ("M-<right>" . markdown-demote))
  (:map markdown-mode-map ("M-S-<left>" . markdown-promote-subtree))
  (:map markdown-mode-map ("M-S-<right>" . markdown-demote-subtree)))

(use-package company)

(use-package eglot
  :config
  (define-key eglot-mode-map
    [remap xref-find-definitions] #'eglot-find-typeDefinition)
  (define-key eglot-mode-map
    [remap xref-find-references] #'eglot-find-declaration)
  (define-key eglot-mode-map (kbd "M-l r") 'eglot-rename)
  (define-key eglot-mode-map (kbd "M-l f") 'eglot-format)

  (add-hook 'c++-mode-hook 'eglot-ensure))

(use-package caddyfile-mode
  :ensure t
  :mode (("Caddyfile\\'" . caddyfile-mode)))

;; *NOTE* Trailing slash important
(setq auto-insert-directory "~/.emacs.d/auto-insert/")

(define-auto-insert "\.cpp" "template.cpp")
(auto-insert-mode)

(defun my/compileandrun()
  (interactive)
  (if (eq major-mode 'c++-mode)
    (let* ((src (file-name-nondirectory (buffer-file-name)))
           (exe (file-name-sans-extension src)))
      (compile (concat "g++ -std=c++17 -O2 -Wall -Wno-sign-compare " src " -o /tmp/" exe " && time /tmp/" exe " < /tmp/input.txt" )))
    (recompile)))

(global-set-key (kbd "<f12>") 'my/compileandrun)

(setq project-switch-use-entire-map t)

(defun my/consult-ripgrep-current-project ()
  "Full text search with ripgrep in current project"
  (interactive)
  (consult-ripgrep (if (project-current) (project-root (project-current))
                     default-directory) ""))
(define-key project-prefix-map (kbd "F") #'my/consult-ripgrep-current-project)

(defun my/project-all-project-files ()
  "Get a list of all files in all known projects."
  (cl-mapcan
   (lambda (project)
     (when (file-exists-p project)
       (mapcar (lambda (file)
                 (expand-file-name file project))
               (project-files (project-current nil project)))))
   (project-known-project-roots)))

(defun my/project-find-file-in-known-projects ()
  "Find a file from all known projects."
  (interactive)
  (let* ((completion-ignore-case read-file-name-completion-ignore-case)
         ;; Note that "project--read-file-cpd-relative" is broken for
         ;; this function since Emacs 29. Instead of using
         ;; "project-read-file-name-function", always use
         ;; "project--read-file-absolute".
         (file (project--read-file-absolute
                "Find file in known projects" (my/project-all-project-files) nil nil
                (thing-at-point 'filename))))
    (if (string= file "")
        (user-error "You didn't specify the file")
      (find-file file))))

(define-key project-prefix-map (kbd "a") #'my/project-find-file-in-known-projects)

(use-package rime
  :init
  (when (eq system-type 'darwin)
    ;; Set the root for librime ("rime-api.h").
    ;; See https://github.com/DogLooksGood/emacs-rime/blob/master/INSTALLATION.org
    (setq rime-librime-root "~/.emacs.d/librime/dist")

    ;; Set the root for emacs module ("emacs-module.h")
    (setq rime-emacs-module-header-root "/opt/homebrew/opt/emacs-head@29/include/"))

  (setq default-input-method "rime")
  :custom
  (rime-show-candidate 'posframe)
  (rime-posframe-style 'vertical))

(setq word-wrap-by-category t)

(use-package cnfonts
  :init
  (if (eq system-type 'darwin)
      (setq cnfonts-profiles '("osx"))
    (setq cnfonts-profiles '("hack")))

  (setq cnfonts-default-fontsize 10)
  :config
  (cnfonts-mode 1))

(use-package pinentry
  :init
  (pinentry-start))

;; These are some key bindings ported from MacOS to everywhere, since I found they are handy.

;; MacOS uses Command+f for "find".
(global-set-key (kbd "M-f") 'consult-line)
(global-set-key (kbd "M-F") 'my/consult-ripgrep-org-directory)

;; MacOS uses Command+s for "save".
(global-set-key (kbd "M-s") 'my/save-buffer)

;; MacOS uses Command+c to copy but I prefer keeping the Emacs style.
;; Disable it in case I mistrigger "capitalize-word".
(global-unset-key (kbd "M-c"))

(when (eq system-type 'darwin)
  ;; MacOS put the menu-bar in the top bar which already using the space.
  (menu-bar-mode 1)

  (setq mac-option-modifier 'alt)
  (setq mac-command-modifier 'meta)

  (global-set-key (kbd "<home>") 'move-beginning-of-line)
  (global-set-key (kbd "<end>") 'move-end-of-line)

  ;; MacOS uses Command+Control+f to toggle fullscreen. Also make it work with Emacs.
  (global-set-key (kbd "C-M-f") 'toggle-frame-fullscreen)

  ;; MacOS uses Option+up/down to scroll.
  (global-set-key (kbd "A-<up>") 'scroll-down-command)
  (global-set-key (kbd "A-<down>") 'scroll-up-command)

  ;; (global-set-key (kbd "M-p") 'execute-extended-command)
  ;; (global-set-key (kbd "M-x") 'kill-region) ; already bind for s-x
  ;; sets fn-delete to be right-delete
  (global-set-key [kp-delete] 'delete-char)

  (defun my/apply-theme (appearance)
    "Load theme, taking current system APPEARANCE into consideration."
    ;; (mapc #'disable-theme custom-enabled-themes)
    (pcase appearance
      ('light (modus-themes-select 'modus-operandi))
      ('dark (modus-themes-select 'modus-vivendi-tinted))))

  (add-hook 'ns-system-appearance-change-functions #'my/apply-theme))

(setq user-mail-address "whhone@gmail.com"
      user-full-name "Wai Hon Law")