;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-

;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>

;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.3.1
;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))

;; This file is NOT part of GNU Emacs.

;; This program is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 3, or (at your option)
;; any later version.
;;
;; This program is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.
;;
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs; see the file COPYING.  If not, write to the
;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301, USA.

;;; Commentary:
;;
;; This module implements `org-roam-mode', which is a major mode that used by
;; special Org-roam buffers to display various content in a section-like manner
;; about the nodes and relevant to them information (e.g. backlinks) with which
;; the user can interact with.
;;
;;; Code:
(require 'org-roam)

;;;; Declarations
(defvar org-ref-buffer-hacked)

;;; Options
(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
                                        #'org-roam-reflinks-section)
  "A list of sections for the `org-roam-mode' based buffers.
Each section is a function that is passed the `org-roam-node'
for which the section will be constructed as the first
argument. Normally this node is `org-roam-buffer-current-node'.
The function may also accept other optional arguments. Each item
in the list is either:

1. A function, which is called only with the `org-roam-node' as the argument
2. A list, containing the function and the optional arguments.

For example, one can add

    (org-roam-backlinks-section :unique t)

to the list to pass :unique t to the section-rendering function."
  :group 'org-roam
  :type `(repeat (choice (symbol :tag "Function")
                         (list :tag "Function with arguments"
                               (symbol :tag "Function")
                               (repeat :tag "Arguments" :inline t (sexp :tag "Arg"))))))

(defcustom org-roam-buffer-postrender-functions (list)
  "Functions to run after the Org-roam buffer is rendered.
Each function accepts no arguments, and is run with the Org-roam
buffer as the current buffer."
  :group 'org-roam
  :type 'hook)

(defcustom org-roam-preview-function #'org-roam-preview-default-function
  "The preview function to use to populate the Org-roam buffer.

The function takes no arguments, but the point is temporarily set
to the exact location of the backlink."
  :group 'org-roam
  :type 'function)

(defcustom org-roam-preview-postprocess-functions (list #'org-roam-strip-comments)
  "A list of functions to postprocess the preview content.

Each function takes a single argument, the string for the preview
content, and returns the post-processed string. The functions are
applied in order of appearance in the list."
  :group 'org-roam
  :type 'hook)

;;; Faces
(defface org-roam-header-line
  `((((class color) (background light))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :foreground "DarkGoldenrod4"
     :weight bold)
    (((class color) (background  dark))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :foreground "LightGoldenrod2"
     :weight bold))
  "Face for the `header-line' in some Org-roam modes."
  :group 'org-roam-faces)

(defface org-roam-title
  '((t :weight bold))
  "Face for Org-roam titles."
  :group 'org-roam-faces)

(defface org-roam-olp
  '((((class color) (background light)) :foreground "grey60")
    (((class color) (background  dark)) :foreground "grey40"))
  "Face for the OLP of the node."
  :group 'org-roam-faces)

(defface org-roam-preview-heading
  `((((class color) (background light))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :background "grey80"
     :foreground "grey30")
    (((class color) (background dark))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :background "grey25"
     :foreground "grey70"))
  "Face for preview headings."
  :group 'org-roam-faces)

(defface org-roam-preview-heading-highlight
  `((((class color) (background light))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :background "grey75"
     :foreground "grey30")
    (((class color) (background dark))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :background "grey35"
     :foreground "grey70"))
  "Face for current preview headings."
  :group 'org-roam-faces)

(defface org-roam-preview-heading-selection
  `((((class color) (background light))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :inherit org-roam-preview-heading-highlight
     :foreground "salmon4")
    (((class color) (background dark))
     ,@(and (>= emacs-major-version 27) '(:extend t))
     :inherit org-roam-preview-heading-highlight
     :foreground "LightSalmon3"))
  "Face for selected preview headings."
  :group 'org-roam-faces)

(defface org-roam-preview-region
  `((t :inherit bold
       ,@(and (>= emacs-major-version 27)
              (list :extend (ignore-errors (face-attribute 'region :extend))))))
  "Face used by `org-roam-highlight-preview-region-using-face'.

This face is overlaid over text that uses other hunk faces,
and those normally set the foreground and background colors.
The `:foreground' and especially the `:background' properties
should be avoided here.  Setting the latter would cause the
loss of information.  Good properties to set here are `:weight'
and `:slant'."
  :group 'org-roam-faces)

(defface org-roam-dim
  '((((class color) (background light)) :foreground "grey60")
    (((class color) (background  dark)) :foreground "grey40"))
  "Face for the dimmer part of the widgets."
  :group 'org-roam-faces)

;;; Major mode
(defvar org-roam-mode-map
  (let ((map (make-sparse-keymap)))
    (set-keymap-parent map magit-section-mode-map)
    (define-key map [C-return]  'org-roam-buffer-visit-thing)
    (define-key map (kbd "C-m") 'org-roam-buffer-visit-thing)
    (define-key map [remap revert-buffer] 'org-roam-buffer-refresh)
    map)
  "Parent keymap for all keymaps of modes derived from `org-roam-mode'.")

(define-derived-mode org-roam-mode magit-section-mode "Org-roam"
  "Major mode for displaying relevant information about Org-roam nodes.
This mode is used by special Org-roam buffers, such as persistent
`org-roam-buffer' and dedicated Org-roam buffers
\(`org-roam-buffer-display-dedicated'), which render the
information in a section-like manner (see
`org-roam-mode-sections'), with which the user can
interact with."
  :group 'org-roam
  (face-remap-add-relative 'header-line 'org-roam-header-line))

;;; Buffers
(defvar org-roam-buffer-current-node nil
  "The node for which an `org-roam-mode' based buffer displays its contents.
This set both, locally and globally. Normally the local value is
only set in the `org-roam-mode' based buffers, while the global
value shows the current node in the persistent `org-roam-buffer'.")

(put 'org-roam-buffer-current-node 'permanent-local t)

(defvar org-roam-buffer-current-directory nil
  "The `org-roam-directory' value of `org-roam-buffer-current-node'.
Set both, locally and globally in the same way as
`org-roam-buffer-current-node'.")

(put 'org-roam-buffer-current-directory 'permanent-local t)

;;;; Library
(defun org-roam-buffer-visit-thing ()
  "This is a placeholder command.
Where applicable, section-specific keymaps bind another command
which visits the thing at point."
  (interactive)
  (user-error "There is no thing at point that could be visited"))

(defun org-roam-buffer-file-at-point (&optional assert)
  "Return the file at point in the current `org-roam-mode' based buffer.
If ASSERT, throw an error."
  (if-let ((file (magit-section-case
                   (org-roam-node-section (org-roam-node-file (oref it node)))
                   (org-roam-grep-section (oref it file))
                   (org-roam-preview-section (oref it file))
                   (t (cl-assert (derived-mode-p 'org-roam-mode))))))
      file
    (when assert
      (user-error "No file at point"))))

(defun org-roam-buffer-refresh ()
  "Refresh the contents of the currently selected Org-roam buffer."
  (interactive)
  (cl-assert (derived-mode-p 'org-roam-mode))
  (save-excursion (org-roam-buffer-render-contents)))

(defun org-roam-buffer-render-contents ()
  "Recompute and render the contents of an Org-roam buffer.
Assumes that the current buffer is an `org-roam-mode' based
buffer."
  (let ((inhibit-read-only t))
    (erase-buffer)
    (org-roam-mode)
    (setq-local default-directory org-roam-buffer-current-directory)
    (setq-local org-roam-directory org-roam-buffer-current-directory)
    (org-roam-buffer-set-header-line-format
     (org-roam-node-title org-roam-buffer-current-node))
    (magit-insert-section (org-roam)
      (magit-insert-heading)
      (dolist (section org-roam-mode-sections)
        (pcase section
          ((pred functionp)
           (funcall section org-roam-buffer-current-node))
          (`(,fn . ,args)
           (apply fn (cons org-roam-buffer-current-node args)))
          (_
           (user-error "Invalid `org-roam-mode-sections' specification")))))
    (run-hooks 'org-roam-buffer-postrender-functions)
    (goto-char 0)))

(defun org-roam-buffer-set-header-line-format (string)
  "Set the header-line using STRING.
If the `face' property of any part of STRING is already set, then
that takes precedence. Also pad the left side of STRING so that
it aligns with the text area."
  (setq-local header-line-format
              (concat (propertize " " 'display '(space :align-to 0))
                      string)))

;;;; Dedicated buffer
;;;###autoload
(defun org-roam-buffer-display-dedicated (node)
  "Launch NODE dedicated Org-roam buffer.
Unlike the persistent `org-roam-buffer', the contents of this
buffer won't be automatically changed and will be held in place.

In interactive calls prompt to select NODE, unless called with
`universal-argument', in which case NODE will be set to
`org-roam-node-at-point'."
  (interactive
   (list (if current-prefix-arg
             (org-roam-node-at-point 'assert)
           (org-roam-node-read nil nil nil 'require-match))))
  (let ((buffer (get-buffer-create (org-roam-buffer--dedicated-name node))))
    (with-current-buffer buffer
      (setq-local org-roam-buffer-current-node node)
      (setq-local org-roam-buffer-current-directory org-roam-directory)
      (org-roam-buffer-render-contents))
    (display-buffer buffer)))

(defun org-roam-buffer--dedicated-name (node)
  "Construct buffer name for NODE dedicated Org-roam buffer."
  (let ((title (org-roam-node-title node))
        (filename (file-relative-name (org-roam-node-file node) org-roam-directory)))
    (format "*org-roam: %s<%s>*" title filename)))

(defun org-roam-buffer-dedicated-p (&optional buffer)
  "Return t if an Org-roam BUFFER is a node dedicated one.
See `org-roam-buffer-display-dedicated' for more details.
If BUFFER is nil, default it to `current-buffer'."
  (or buffer (setq buffer (current-buffer)))
  (string-match-p (concat "^" (regexp-quote "*org-roam: "))
                  (buffer-name buffer)))

;;;; Persistent buffer
(defvar org-roam-buffer "*org-roam*"
  "The persistent Org-roam buffer name. Must be surround with \"*\".
The content inside of this buffer will be automatically updated
to the nearest node at point that comes from the current buffer.
To toggle its display use `org-roam-buffer-toggle' command.")

(defun org-roam-buffer-toggle ()
  "Toggle display of the persistent `org-roam-buffer'."
  (interactive)
  (pcase (org-roam-buffer--visibility)
    ('visible
     (progn
       (quit-window nil (get-buffer-window org-roam-buffer))
       (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
    ((or 'exists 'none)
     (progn
       (display-buffer (get-buffer-create org-roam-buffer))
       (org-roam-buffer-persistent-redisplay)))))

(define-inline org-roam-buffer--visibility ()
  "Return the current visibility state of the persistent `org-roam-buffer'.
Valid states are `visible', `exists' and `none'."
  (declare (side-effect-free t))
  (inline-quote
   (cond
    ((get-buffer-window org-roam-buffer) 'visible)
    ((get-buffer org-roam-buffer) 'exists)
    (t 'none))))

(defun org-roam-buffer-persistent-redisplay ()
  "Recompute contents of the persistent `org-roam-buffer'.
Has no effect when there's no `org-roam-node-at-point'."
  (when-let ((node (org-roam-node-at-point)))
    (unless (equal node org-roam-buffer-current-node)
      (setq org-roam-buffer-current-node node
            org-roam-buffer-current-directory org-roam-directory)
      (with-current-buffer (get-buffer-create org-roam-buffer)
        (org-roam-buffer-render-contents)
        (add-hook 'kill-buffer-hook #'org-roam-buffer--persistent-cleanup-h nil t)))))

(defun org-roam-buffer--persistent-cleanup-h ()
  "Clean-up global state that's dedicated for the persistent `org-roam-buffer'."
  (setq-default org-roam-buffer-current-node nil
                org-roam-buffer-current-directory nil))

(add-hook 'org-roam-find-file-hook #'org-roam-buffer--setup-redisplay-h)
(defun org-roam-buffer--setup-redisplay-h ()
  "Setup automatic redisplay of the persistent `org-roam-buffer'."
  (add-hook 'post-command-hook #'org-roam-buffer--redisplay-h nil t))

(defun org-roam-buffer--redisplay-h ()
  "Reconstruct the persistent `org-roam-buffer'.
This needs to be quick or infrequent, because this designed to
run at `post-command-hook'."
  (and (get-buffer-window org-roam-buffer)
       (org-roam-buffer-persistent-redisplay)))

;;; Sections
;;;; Node
(defvar org-roam-node-map
  (let ((map (make-sparse-keymap)))
    (set-keymap-parent map org-roam-mode-map)
    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-node-visit)
    map)
  "Keymap for `org-roam-node-section's.")

(defclass org-roam-node-section (magit-section)
  ((keymap :initform 'org-roam-node-map)
   (node :initform nil))
  "A `magit-section' used by `org-roam-mode' to outline NODE in its own heading.")

(cl-defun org-roam-node-insert-section (&key source-node point properties)
  "Insert section for a link from SOURCE-NODE to some other node.
The other node is normally `org-roam-buffer-current-node'.

SOURCE-NODE is an `org-roam-node' that links or references with
the other node.

POINT is a character position where the link is located in
SOURCE-NODE's file.

PROPERTIES (a plist) contains additional information about the
link.

Despite the name, this function actually inserts 2 sections at
the same time:

1. `org-roam-node-section' for a heading that describes
   SOURCE-NODE. Acts as a parent section of the following one.

2. `org-roam-preview-section' for a preview content that comes
   from SOURCE-NODE's file for the link (that references the
   other node) at POINT. Acts a child section of the previous
   one."
  (magit-insert-section section (org-roam-node-section)
    (let ((outline (if-let ((outline (plist-get properties :outline)))
                       (mapconcat #'org-link-display-format outline " > ")
                     "Top")))
      (insert (concat (propertize (org-roam-node-title source-node)
                                  'font-lock-face 'org-roam-title)
                      (format " (%s)"
                              (propertize outline 'font-lock-face 'org-roam-olp)))))
    (magit-insert-heading)
    (oset section node source-node)
    (magit-insert-section section (org-roam-preview-section)
      (insert (org-roam-fontify-like-in-org-mode
               (org-roam-preview-get-contents (org-roam-node-file source-node) point))
              "\n")
      (oset section file (org-roam-node-file source-node))
      (oset section point point)
      (insert ?\n))))

;;;; Preview
(defvar org-roam-preview-map
  (let ((map (make-sparse-keymap)))
    (set-keymap-parent map org-roam-mode-map)
    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-preview-visit)
    map)
  "Keymap for `org-roam-preview-section's.")

(defclass org-roam-preview-section (magit-section)
  ((keymap :initform 'org-roam-preview-map)
   (file :initform nil)
   (point :initform nil))
  "A `magit-section' used by `org-roam-mode' to contain preview content.
The preview content comes from FILE, and the link as at POINT.")

(defun org-roam-preview-visit (file point &optional other-window)
  "Visit FILE at POINT and return the visited buffer.
With OTHER-WINDOW non-nil do so in another window.
In interactive calls OTHER-WINDOW is set with
`universal-argument'."
  (interactive (list (org-roam-buffer-file-at-point 'assert)
                     (oref (magit-current-section) point)
                     current-prefix-arg))
  (let ((buf (find-file-noselect file))
        (display-buffer-fn (if other-window
                               #'switch-to-buffer-other-window
                             #'pop-to-buffer-same-window)))
    (funcall display-buffer-fn buf)
    (with-current-buffer buf
      (widen)
      (goto-char point))
    (when (org-invisible-p) (org-fold-show-context))
    buf))

(defun org-roam-preview-default-function ()
  "Return the preview content at point.

This function returns the all contents under the current
headline, up to the next headline."
  (let ((beg (save-excursion
               (org-roam-end-of-meta-data t)
               (point)))
        (end (save-excursion
               (org-next-visible-heading 1)
               (point))))
    (string-trim (buffer-substring-no-properties beg end))))

(defun org-roam-preview-get-contents (file pt)
  "Get preview content for FILE at PT."
  (save-excursion
    (org-roam-with-temp-buffer file
      (org-with-wide-buffer
       (goto-char pt)
       (let ((s (funcall org-roam-preview-function)))
         (dolist (fn org-roam-preview-postprocess-functions)
           (setq s (funcall fn s)))
         s)))))

;;;; Backlinks
(cl-defstruct (org-roam-backlink (:constructor org-roam-backlink-create)
                                 (:copier nil))
  source-node target-node
  point properties)

(cl-defmethod org-roam-populate ((backlink org-roam-backlink))
  "Populate BACKLINK from database."
  (setf (org-roam-backlink-source-node backlink)
        (org-roam-populate (org-roam-backlink-source-node backlink))
        (org-roam-backlink-target-node backlink)
        (org-roam-populate (org-roam-backlink-target-node backlink)))
  backlink)

(cl-defun org-roam-backlinks-get (node &key unique)
  "Return the backlinks for NODE.

 When UNIQUE is nil, show all positions where references are found.
 When UNIQUE is t, limit to unique sources."
  (let* ((sql (if unique
                  [:select :distinct [source dest pos properties]
                   :from links
                   :where (= dest $s1)
                   :and (= type "id")
                   :group :by source
                   :having (funcall min pos)]
                [:select [source dest pos properties]
                 :from links
                 :where (= dest $s1)
                 :and (= type "id")]))
         (backlinks (org-roam-db-query sql (org-roam-node-id node))))
    (cl-loop for backlink in backlinks
             collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
                       (org-roam-populate
                        (org-roam-backlink-create
                         :source-node (org-roam-node-create :id source-id)
                         :target-node (org-roam-node-create :id dest-id)
                         :point pos
                         :properties properties))))))

(defun org-roam-backlinks-sort (a b)
  "Default sorting function for backlinks A and B.
Sorts by title."
  (string< (org-roam-node-title (org-roam-backlink-source-node a))
           (org-roam-node-title (org-roam-backlink-source-node b))))

(cl-defun org-roam-backlinks-section (node &key (unique nil) (show-backlink-p nil)
                                           (section-heading "Backlinks:"))
  "The backlinks section for NODE.

When UNIQUE is nil, show all positions where references are found.
When UNIQUE is t, limit to unique sources.

When SHOW-BACKLINK-P is not null, only show backlinks for which
this predicate is not nil.

SECTION-HEADING is the string used as a heading for the backlink section."
  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node :unique unique))))
    (magit-insert-section (org-roam-backlinks)
      (magit-insert-heading section-heading)
      (dolist (backlink backlinks)
        (when (or (null show-backlink-p)
                  (and (not (null show-backlink-p))
                       (funcall show-backlink-p backlink)))
          (org-roam-node-insert-section
           :source-node (org-roam-backlink-source-node backlink)
           :point (org-roam-backlink-point backlink)
           :properties (org-roam-backlink-properties backlink))))
      (insert ?\n))))

;;;; Reflinks
(cl-defstruct (org-roam-reflink (:constructor org-roam-reflink-create)
                                (:copier nil))
  source-node ref
  point properties)

(cl-defmethod org-roam-populate ((reflink org-roam-reflink))
  "Populate REFLINK from database."
  (setf (org-roam-reflink-source-node reflink)
        (org-roam-populate (org-roam-reflink-source-node reflink)))
  reflink)

(defun org-roam-reflinks-get (node)
  "Return the reflinks for NODE."
  (let ((refs (org-roam-db-query [:select :distinct [refs:ref links:source links:pos links:properties]
                                  :from refs
                                  :left-join links
                                  :where (= refs:node-id $s1)
                                  :and (= links:dest refs:ref)
                                  :union
                                  :select :distinct [refs:ref citations:node-id
                                                     citations:pos citations:properties]
                                  :from refs
                                  :left-join citations
                                  :where (= refs:node-id $s1)
                                  :and (= citations:cite-key refs:ref)]
                                 (org-roam-node-id node)))
        links)
    (pcase-dolist (`(,ref ,source-id ,pos ,properties) refs)
      (push (org-roam-populate
             (org-roam-reflink-create
              :source-node (org-roam-node-create :id source-id)
              :ref ref
              :point pos
              :properties properties)) links))
    links))

(defun org-roam-reflinks-sort (a b)
  "Default sorting function for reflinks A and B.
Sorts by title."
  (string< (org-roam-node-title (org-roam-reflink-source-node a))
           (org-roam-node-title (org-roam-reflink-source-node b))))

(defun org-roam-reflinks-section (node)
  "The reflinks section for NODE."
  (when-let ((refs (org-roam-node-refs node))
             (reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
    (magit-insert-section (org-roam-reflinks)
      (magit-insert-heading "Reflinks:")
      (dolist (reflink reflinks)
        (org-roam-node-insert-section
         :source-node (org-roam-reflink-source-node reflink)
         :point (org-roam-reflink-point reflink)
         :properties (org-roam-reflink-properties reflink)))
      (insert ?\n))))

;;;; Grep
(defvar org-roam-grep-map
  (let ((map (make-sparse-keymap)))
    (set-keymap-parent map org-roam-mode-map)
    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-grep-visit)
    map)
  "Keymap for Org-roam grep result sections.")

(defclass org-roam-grep-section (magit-section)
  ((keymap :initform 'org-roam-grep-map)
   (file :initform nil)
   (row :initform nil)
   (col :initform nil))
  "A `magit-section' used by `org-roam-mode' to contain grep output.")

(defun org-roam-grep-visit (file &optional other-window row col)
  "Visit FILE at row ROW (if any) and column COL (if any). Return the buffer.
With OTHER-WINDOW non-nil (in interactive calls set with
`universal-argument') display the buffer in another window
instead."
  (interactive (list (org-roam-buffer-file-at-point t)
                     current-prefix-arg
                     (oref (magit-current-section) row)
                     (oref (magit-current-section) col)))
  (let ((buf (find-file-noselect file))
        (display-buffer-fn (if other-window
                               #'switch-to-buffer-other-window
                             #'pop-to-buffer-same-window)))
    (funcall display-buffer-fn buf)
    (with-current-buffer buf
      (widen)
      (goto-char (point-min))
      (when row
        (forward-line (1- row)))
      (when col
        (forward-char (1- col))))
    (when (org-invisible-p) (org-fold-show-context))
    buf))

;;;; Unlinked references
(defvar org-roam-unlinked-references-result-re
  (rx (group (one-or-more anything))
      ":"
      (group (one-or-more digit))
      ":"
      (group (one-or-more digit))
      ":"
      (group (zero-or-more anything)))
  "Regex for the return result of a ripgrep query.")

(defun org-roam-unlinked-references-preview-line (file row)
  "Return the preview line from FILE.
This is the ROW within FILE."
  (with-temp-buffer
    (insert-file-contents file)
    (forward-line (1- row))
    (buffer-substring-no-properties
     (save-excursion
       (beginning-of-line)
       (point))
     (save-excursion
       (end-of-line)
       (point)))))

(defun org-roam-unlinked-references--rg-command (titles temp-file)
  "Return the ripgrep command searching for TITLES using TEMP-FILE for pattern.
This avoids shell escaping issues by writing the pattern to a file instead
of passing it directly through the shell command line."
  ;; Write pattern to temp file to avoid shell escaping issues with quotes,
  ;; spaces, and other special characters in titles
  (with-temp-file temp-file
    (insert "\\[([^[]]++|(?R))*\\]"
            (mapconcat (lambda (title)
                         ;; Use regexp-quote instead of shell-quote-argument
                         ;; since we're writing a regex pattern, not a shell argument
                         (format "|(\\b%s\\b)" (regexp-quote title)))
                       titles "")))

  (concat "rg --follow --only-matching --vimgrep --pcre2 --ignore-case "
          (mapconcat (lambda (glob) (concat "--glob " glob))
                     (org-roam--list-files-search-globs org-roam-file-extensions)
                     " ")
          " --file " (shell-quote-argument temp-file) " "
          (shell-quote-argument (expand-file-name org-roam-directory))))

(defun org-roam-unlinked-references-section (node)
  "The unlinked references section for NODE.
References from FILE are excluded."
  (when (and (executable-find "rg")
             (org-roam-node-title node)
             (not (string-match "PCRE2 is not available"
                                (shell-command-to-string "rg --pcre2-version"))))
    (let* ((titles (cons (org-roam-node-title node)
                         (org-roam-node-aliases node)))
           ;; Create temp file for the regex pattern
           (temp-file (make-temp-file "org-roam-rg-pattern-"))
           (rg-command (org-roam-unlinked-references--rg-command titles temp-file)))
      ;; Use unwind-protect to ensure temp file cleanup even if errors occur
      (unwind-protect
          (let* ((results (split-string (shell-command-to-string rg-command) "\n"))
                 f row col match)
            (magit-insert-section (unlinked-references)
              (magit-insert-heading "Unlinked References:")
              (dolist (line results)
                (save-match-data
                  (when (string-match org-roam-unlinked-references-result-re line)
                    (setq f (match-string 1 line)
                          row (string-to-number (match-string 2 line))
                          col (string-to-number (match-string 3 line))
                          match (match-string 4 line))
                    (when (and match
                               (not (file-equal-p (org-roam-node-file node) f))
                               (member (downcase match) (mapcar #'downcase titles)))
                      (magit-insert-section section (org-roam-grep-section)
                        (oset section file f)
                        (oset section row row)
                        (oset section col col)
                        (insert (propertize (format "%s:%s:%s"
                                                    (truncate-string-to-width (file-name-base f) 15 nil nil t)
                                                    row col) 'font-lock-face 'org-roam-dim)
                                " "
                                (org-roam-fontify-like-in-org-mode
                                 (org-roam-unlinked-references-preview-line f row))
                                "\n"))))))
              (insert ?\n)))
        ;; Clean up temp file - this runs even if an error occurs above
        (delete-file temp-file)))))

(provide 'org-roam-mode)
;;; org-roam-mode.el ends here