[elpa] externals/org-remark 91d7583495 065/173: add: mark deactivate-mark & set-buffer-modified-p

[ELPA Syncer]

branch: externals/org-remark
commit 91d758349562c09c9edc668b6482f41798a65b51
Author: Noboru Ota <me@nobiot.com>
Commit: Noboru Ota <me@nobiot.com>

    add: mark deactivate-mark & set-buffer-modified-p
    
    Deactivate the marked region after highlight is applied.
    Also mark will turn the buffer modified for save.
---
 org-marginalia.el | 1435 +++++++++++++++++++++++++++--------------------------
 1 file changed, 720 insertions(+), 715 deletions(-)

diff --git a/org-marginalia.el b/org-marginalia.el
index a49d170aae..ba48ee36a8 100644
--- a/org-marginalia.el
+++ b/org-marginalia.el
@@ -1,715 +1,720 @@
-;;; org-marginalia.el --- highlight & annotate       -*- lexical-binding: t; 
-*-
-
-;; Copyright (C) 2020 Noboru Ota
-
-;; Author: Noboru Ota <me@nobiot.com>
-;; URL: https://github.com/nobiot/org-marginalia
-;; Version: 0.0.5
-;; Last Modified: 2021-01-05
-;; Package-Requires: ((emacs "27.1") (org "9.4"))
-;; Keywords: org-mode, annotation, writing, note-taking, margin-notes
-
-;; 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 of the License, 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 this program.  If not, see <http://www.gnu.org/licenses/>.
-
-;;; Commentary:
-
-;; This package lets you write margin notes (marginalia) for any text file in
-;; a separate Org file.
-
-;;;; Installation
-
-;;;;; MELPA
-
-;; This package is not available on MELPA. Manual installation required.
-
-;;;;; Manual
-
-;; Install these required packages:
-
-;; Ensure to have Org Mode 9.4 or later (tested on 9.4).  This package uses
-;; `org-collect-keywords', which does not exist in an earlier version.
-
-;; Then put this file in your load-path, and put this in your init
-;; file:
-;; (require 'org-marginalia)
-
-;;;; Usage
-
-;; - `org-marginalia-mode' ::
-;; Org-marginalia is a local minor mode. Toggle it on/off with using
-;; `org-marginalia-mode'. On activating, it loads your saved highlighters from
-;; the marginalia file, and enables automatic saving of highlighters. The
-;; automatic saving is achieved via function `org-marginalia-save' added to
-;; `after-save-hook'.
-
-;; - `org-marginalia-mark' (C-c n m by default) ::
-;; Select a region of text, and call `org-marginalia-mark' (bound to C-c n m 
by default)
-;; to highlight the region. It will generate a new ID, and start tracking the
-;; location -- so you can edit text around the marked text. Do not copy and
-;; paste as it will disappear and it is a bit tricky to recover the
-;; highlighter. To create a new margin note entry in themarginalia file, save 
the buffer.
-
-;; - `org-marginalia-save' ::
-;; By default, Org-marginalia creates or updates the highlighter's location
-;; and text inside automatically in the marginalia file. You can manually call
-;; `org-marginalia-save' to manually do it (automatic process also call this 
command).
-
-;; - `org-marginalia-open' (C-c o by default) ::
-;; Move your cursor on the highlighted text, and call `org-marginalia-open' to 
open the
-;; relevant margin notes in a separate window. Your cursor should move to the
-;; marginalia buffer narrowed to the relevant margin notes entry. You can edit
-;; the margin notes as a normal Org file. Once you have done editing, you can
-;; simply save and close the buffer (kill or close the window) as per your
-;; normal workflow. Technically, the marginalia buffer is a cloned indirect
-;; buffer of the marginalia file.
-
-;; - `org-marginalia-load' ::
-;; This command open the marginalia file and load the saved highlights onto
-;; current buffer. If there is no margin notes for it, it will output a
-;; message in the echo. Highlights tracked locally by this packages cannot
-;; persist when you kill the buffer, or quit Emacs. When you re-launch Emacs,
-;; ensure to turn on `org-marginalia-mode' to load the highlights. Load is
-;; automatically done when you activate the minor mode.
-
-;; - `org-marginalia-remove' ::
-;; This command removes the highlight at point. It will remove the highlight,
-;; and remove the properties from the marginalia, but will keep the headline
-;; and notes in tact.
-;;
-;; You can pass a universal argument with
-;; \\[universal-argument] (ARG). If this is the case, the command
-;; additionally deletes the entire heading subtree, along with the
-;; notes you have written, for the highlight."
-
-;; - `org-marginalia-next' (C-c n ] by default) ::
-;; Move to the next highlight if any. If there is none below the cursor, and
-;; there is a highlight above, loop back to the top one.
-
-;; If the point has moved to the next highlight, this function enables
-;; transient map with `set-transient-map'. You don't have to press the
-;; keybinding prefix again to move further to the next. That is, you can do a
-;; key sequence like this (assuming `org-marginalia-next' is bound to C-c n):
-
-;;   C-c n ] ] ] ]
-
-;; If you have the same prefix for `org-marginalia-prev', you can combine it 
in the
-;; sequence like so:
-
-;;  C-c n ] ] [ [
-;;  This lets your cursor back to where you started (next next prev prev)
-
-;; - `org-marginalia-prev' (C-c n [ by default) :: Move to the previous 
highlight if any.
-;; If there is none above the cursor, and there is a highlight below, loop
-;; back to the bottom one. This function enables transient map. See 
`org-marginalia-next'
-;; for detail.
-
-;; - `org-marginalia-toggle' ::
-;; Toggle showing/hiding of highlighters in current buffer. It only affects
-;; the display of the highlighters. When hidden, highlights' locations are
-;; still kept tracked; thus, upon buffer-save the correct locations are still
-;; recorded in the marginalia file.
-
-;;;; Customizing
-
-;; - Highlighter face can be changed via `org-marginalia-highlighter'
-;; - Marginalia file is defined with `org-marginalia-notes-file-path'
-
-;;;; Known Limitations
-
-;; - Turning off minor mode does not turn off the highlighters
-;;   This should not do any harm, but if you are distracted, kill the buffer
-;;   (not revert) and visit it again. Toggling show/hide of highlighters is
-;;   something I - would like to add later.
-
-;; - Copy & pasting loses highlights
-;;   You could mqanually recover it by adjusting the properties in the
-;;   marginalia file.
-
-;;;; Credits
-
-;; To create this package, I was inspired by the following packages. I did not
-;; copy any part of them, but borrowed some ideas from them -- e.g. saving the
-;; margin notes in a separate file.
-
-;; - [[https://github.com/jkitchin/ov-highlight][ov-highlight]]
-;;   John Kitchin's (author of Org-ref). Great UX for markers with hydra.
-;;   Saves the marker info and comments directly within the Org file as Base64
-;;   encoded string. It uses overlays.
-
-;; - [[https://github.com/bastibe/annotate.el][Annotate.el]]
-;;   Bastian Bechtold's (author of Org-journal). Unique display of annotations
-;;   right next to (or on top of) the text. It seems to be designed for very
-;;   short annotations, and perhaps for code review (programming practice); I
-;;   have seen recent issues reported when used with variable-pitch fonts
-;;   (prose).
-
-;; - 
[[https://github.com/tkf/org-mode/blob/master/contrib/lisp/org-annotate-file.el][Org-annotate-file]]
-;;   Part of Org's contrib library. It seems to be designed to annotate a
-;;   whole file in a separate Org file, rather than specific text items
-
-;; - [[https://github.com/IdoMagal/ipa.el][InPlaceAnnotations (ipa-mode)]]
-;;   It looks similar to Annotate.el above
-
-;;; Code:
-
-;;;; Requirements
-
-(require 'org)
-(require 'org-id)
-(declare-function org-collect-keywords 'org)
-
-;;;; Customization
-
-(defgroup org-marginalia nil
-  "Write margin notes (marginalia) for any text file in a
-separate Org file"
-  :group 'org
-  :prefix "org-marginalia-"
-  :link '(url-link :tag "Github" "https://github.com/nobiot/org-marginalia";))
-
-(defface org-marginalia-highlighter
-  '((((class color) (min-colors 88) (background light))
-     :underline "#aecf90" :background "#ecf7ed")
-    (((class color) (min-colors 88) (background dark))
-     :underline "#00422a" :background "#001904")
-    (t
-     :inherit highlight))
-  "Face for highlighters."
-  :group 'org-marginalia)
-
-(defcustom org-marginalia-notes-file-path "marginalia.org"
-  "Specify the file path for the marginalia.org file.
-The default is \"./marginalia.org\", thus one marginalia file per directory.
-Ensure that it is an Org file."
-  :type 'string
-  :group 'org-marginalia)
-
-(defcustom org-marginalia-tracking-file
-  (locate-user-emacs-file ".org-marginalia-tracking" nil)
-  "File name where the files `org-marginalia' tracks is saved.
-When `org-marginalia-global-tracking-mode' is active, opening a file
-saved in `org-marginalia-tracking-file' automatically loads highlights."
-  :type 'file)
-
-;;;; Variables
-
-(defvar-local org-marginalia-loaded nil)
-
-(defvar-local org-marginalia-highlights '()
-  "Keep track of all the highlights.
-It is a local variable and is a list of multiple highlights.
-Each element is an overlay representing a highlighted text region.
-
-On save-buffer each highlight will be persisted in the marginalia file
-(defined by `org-marginalia-notes-file-path').")
-
-(defvar org-marginalia-last-notes-buffer nil
-  "Stores the cloned indirect buffer for the margin notes.
-It is meant to exist only one of these in each Emacs session.")
-
-(defvar org-marginalia-tracking-file-loaded nil)
-
-(defvar org-marginalia-files-tracked nil)
-
-;; Const for the names of properties in Org Mode
-(defconst org-marginalia-prop-id "marginalia-id")
-(defconst org-marginalia-prop-source-file "marginalia-source-file")
-(defconst org-marginalia-prop-source-beg "marginalia-source-beg")
-(defconst org-marginalia-prop-source-end "marginalia-source-end")
-
-;;;; Commands
-
-;;;###autoload
-(define-minor-mode org-marginalia-global-tracking-mode
-  "Global mode. When enabled, check files saved in
-`org-marginalia-tracking-file' and opening them automatically
-activates `org-marginalia-mode' locally for the file opened."
-  :init-value nil
-  :lighter " marginalia-tracking"
-  :global t
-  (cond
-   (org-marginalia-global-tracking-mode
-    ;; Activate
-    (when (and (not org-marginalia-tracking-file-loaded)
-              (file-exists-p org-marginalia-tracking-file))
-      (org-marginalia-tracking-load))
-    (add-hook 'find-file-hook #'org-marginalia-tracking-auto-on)
-    (add-hook 'kill-emacs-hook #'org-marginalia-tracking-save))
-   (t
-    ;; dactivate
-    (setq org-marginalia-files-tracked nil)
-    (setq org-marginalia-tracking-file-loaded nil)
-    (remove-hook 'find-file-hook #'org-marginalia-tracking-auto-on)
-    (remove-hook 'kill-emacs-hook #'org-marginalia-tracking-save))))
-
-(defun org-marginalia-tracking-auto-on ()
-  (when (and org-marginalia-files-tracked
-            (member (abbreviate-file-name (buffer-file-name))
-                    org-marginalia-files-tracked))
-    (org-marginalia-mode +1)))
-
-(defun org-marginalia-tracking-load ()
-  ".
-Each line. It loads regardless of `org-marginalia-tracking-file';
-if already loaded this function reloads."
-  (with-temp-buffer
-    (condition-case nil
-       (progn
-         (insert-file-contents org-marginalia-tracking-file)
-         (setq org-marginalia-files-tracked
-               (split-string (buffer-string) "\n"))
-          (setq org-marginalia-tracking-file-loaded t)))))
-
-(defun org-marginalia-tracking-save ()
-  "."
-  (interactive)
-  (when org-marginalia-files-tracked
-    (with-temp-file org-marginalia-tracking-file
-      (insert (mapconcat 'identity org-marginalia-files-tracked "\n")))))
-
-;;;###autoload
-(define-minor-mode org-marginalia-mode
-    "Highlight text, write margin notes for any text file in Org Mode.
-
-This command toggles Org-marginalia local minor mode. On
-activation, it loads your saved highlights from the marginalia
-file, and enables automatic saving of highlights.
-
-The automatic saving is achieved via function
-`org-marginalia-save' added to `after-save-hook'.
-
-Interactively with no argument, this command toggles the mode. A
-positive prefix argument enables the mode, any other prefix
-argument disables it. From Lisp, argument omitted or nil enables
-the mode, `toggle' toggles the state.
-
-\\{org-marginalia-mode-map}"
-    :init-value nil
-    :lighter " marginalia"
-    :global nil
-    :keymap (let ((map (make-sparse-keymap)))
-              map)
-    (cond
-     (org-marginalia-mode
-      ;; Activate
-      (org-marginalia-load)
-      (add-hook 'after-save-hook #'org-marginalia-save nil t))
-     (t
-      ;; Deactivate
-      (when org-marginalia-highlights
-       (dolist (highlight org-marginalia-highlights)
-         (delete-overlay highlight)))
-      (setq org-marginalia-highlights nil)
-      (setq org-marginalia-loaded nil)
-      (remove-hook 'after-save-hook #'org-marginalia-save t))))
-
-;;;###autoload
-(defun org-marginalia-mark (beg end &optional id)
-  "Highlight the selected region (BEG and END).
-When used interactively. it will generate a new ID, always
-assuming it is a new highlighted text region, and start tracking
-the higlight's location, so that you can edit the text around.
-
-It will not create a marginalia entry yet. Call `org-marginalia-save' to
-create a new entry (it is automatic with `after-save-hook').
-
-When this function is called from Elisp, ID can be optionally
-passed. If so, no new ID gets generated.
-
-Every highlighted texts in the local buffer is tracked by
-`org-marginalia-highlights' local variable. The highlght is sorted by the
-beginning point in the ascending; this is useful for `org-marginalia-next'
-and `org-marginalia-prev'."
-  (interactive "r")
-  ;; Ensure to turn on the local minor mode
-  (unless org-marginalia-mode (org-marginalia-mode +1))
-  ;; UUID is too long; does not have to be the full length
-  (when (not id) (setq id (substring (org-id-uuid) 0 8)))
-  ;; Add highlight to the text
-  (org-with-wide-buffer
-   (let ((ov (make-overlay beg end)))
-     (overlay-put ov 'face 'org-marginalia-highlighter)
-     (overlay-put ov 'org-marginalia-id id)
-     ;; Keep track in a local variable It's a list overlays, guranteed to
-     ;; contain only marginalia overlays.
-
-     ;; TODO Do we need to consider this for overlay?
-     ;; `set-marker-insertion-type' to
-     ;; set the type t is necessary to move the cursor in sync with the
-     ;; font-lock-face property of the text property.
-     (push ov org-marginalia-highlights)))
-  (org-marginalia-sort-highlights-list))
-
-;;;###autoload
-(defun org-marginalia-load ()
-  "Open the marginalia file and load the saved highlights onto current buffer.
-If there is no margin notes for it, it will output a message in
-the echo.
-
-Highlights tracked locally by this packages cannot persist when
-you kill the buffer, or quit Emacs. When you re-launch Emacs,
-ensure to turn on `org-marginalia-mode' to load the highlights.
-Load is automatically done when you activate the minor mode."
-  (interactive)
-  ;; Open the marginalia file
-  ;; Read all the positions
-  (unless org-marginalia-mode (org-marginalia-mode +1))
-  (unless org-marginalia-loaded
-    (when-let* ((filename (buffer-file-name))
-               (margin-buf (find-file-noselect org-marginalia-notes-file-path))
-               (source-path (abbreviate-file-name filename)))
-      ;; Get hilights: each highlighlight is stored as an alist
-      ;; (id beg . end)
-      ;; TODO check if there is any relevant notes for the current file
-      (let ((highlights '()))
-       (with-current-buffer margin-buf
-          (org-with-wide-buffer
-           (let ((heading (org-find-property
-                          org-marginalia-prop-source-file source-path)))
-             (if (not heading)
-                (message "No marginalia written for %s." source-path)
-               (goto-char (org-find-property
-                          org-marginalia-prop-source-file source-path))
-               ;; Narrow to only subtree for a single file
-               ;; `org-find-property' ensures that it is the beginning of H1
-               (org-narrow-to-subtree)
-               ;; It's important that the headline levels are fixed
-               ;; H1: File
-               ;; H2: Higlighted region (each one has a dedicated H2 subtree)
-               (while (not (org-next-visible-heading 1))
-                (when-let ((id (org-entry-get (point) "marginalia-id"))
-                            (beg (string-to-number
-                                 (org-entry-get (point)
-                                                "marginalia-source-beg")))
-                            (end (string-to-number
-                                 (org-entry-get (point)
-                                                "marginalia-source-end"))))
-                   (push (cons id (cons beg end)) highlights)))))))
-       ;; Back to the current buffer
-       ;; Look highilights and add highlights to the current buffer
-       (dolist (highlight highlights)
-          (let ((id (car highlight))
-               (beg (car (cdr highlight)))
-               (end (cdr (cdr highlight))))
-            (org-marginalia-mark beg end id)))))
-    (setq org-marginalia-loaded t)))
-
-(defun org-marginalia-save ()
-  "Save all the highlights tracked in current buffer to marginalia file.
-The marginalia file is defined in `org-marginalia-notes-file-path' variable.
-
-This funcion is automatically called when you save the buffer. This is
-achieved via `after-save-hook' (added via `org-marginalia-mode' when you
-activate the minor mode).
-
-`org-marginalia-highlights' is the local variable that tracks every highlight
-in the current buffer. Each highlight is represented by this data structure:
-
-   (id beg-marker . end-marker)"
-  (interactive)
-  (let* ((filename (buffer-file-name))
-         (source-path (abbreviate-file-name filename))
-         (title (or (car (cdr (assoc "TITLE" (org-collect-keywords 
'("TITLE")))))
-                    (file-name-sans-extension (file-name-nondirectory 
(buffer-file-name))))))
-    (dolist (highlight org-marginalia-highlights)
-      (org-marginalia-save-single-highlight highlight title source-path))
-    ;; Tracking
-    (when org-marginalia-files-tracked
-      (add-to-list 'org-marginalia-files-tracked (abbreviate-file-name 
(buffer-file-name))))))
-
-(defun org-marginalia-open (point)
-  "Open the margin notes at POINT, narrowed to the relevant headline.
-It creates a cloned indirect buffer of the marginalia file
-\(`org-marginalia-notes-file-path'\). You can edit the margin notes as a
-normal Org file. Once you have done editing, you can simply save and close the
-buffer (kill or close the window) as per your normal workflow.
-
-This package ensures that there is only one cloned buffer for marginalia by
-tracking it."
-  (interactive "d")
-  (when (buffer-live-p org-marginalia-last-notes-buffer)
-    (kill-buffer org-marginalia-last-notes-buffer))
-  (when-let ((id (get-char-property point 'org-marginalia-id))
-             (ibuf (make-indirect-buffer
-                   (find-file-noselect org-marginalia-notes-file-path) 
"*marginalia*" 'clone)))
-    (setq org-marginalia-last-notes-buffer ibuf)
-    (org-switch-to-buffer-other-window ibuf)
-    (widen)(goto-char (point-min))
-    (when (org-find-property org-marginalia-prop-id id)
-      (goto-char (org-find-property org-marginalia-prop-id id))
-      (org-narrow-to-subtree))))
-
-(defun org-marginalia-remove (point &optional arg)
-  "Remove the highlight at POINT.
-It will remove the highlight, and remove the properties from the
-marginalia, but will keep the headline and notes.
-
-You can pass a universal argument with
-\\[universal-argument] (ARG). If this is the case, the command
-additionally deletes the entire heading subtree, along with the
-notes you have written, for the highlight."
-  (interactive "d\nP")
-  ;; TODO There may be multple overlays
-  (when-let* ((id (get-char-property point 'org-marginalia-id)))
-    ;; Remove the highlight overlay and id
-    (dolist (ov (overlays-at (point)))
-      (when (overlay-get ov 'org-marginalia-id)
-       (delete ov org-marginalia-highlights)
-       (delete-overlay ov)))
-    ;; Remove the element in the variable org-marginalia-highlights
-    ;; TODO need to go through this org-marginalia-hightlights stuff
-    (org-marginalia-sort-highlights-list)
-    ;; Update the marginalia note file accordingly
-    (with-current-buffer (find-file-noselect org-marginalia-notes-file-path)
-      (org-with-wide-buffer
-       (when-let ((id-headline (org-find-property org-marginalia-prop-id id)))
-         (goto-char id-headline)
-        (org-narrow-to-subtree)
-         (org-delete-property org-marginalia-prop-id)
-         (org-delete-property org-marginalia-prop-source-beg)
-         (org-delete-property org-marginalia-prop-source-end)
-         (when arg
-           ;; TODO I would love to add the y-n prompt if there is any notes 
written
-           (delete-region (point-min)(point-max))
-           (message "Deleted the marginal notes.")))))
-    t))
-
-(defun org-marginalia-next ()
-  "Look at the current point, and move to the next highlight, if any.
-If there is none below the point, but there is a highlight in the
-buffer, go back to the first one.
-
-If the point has moved to the next highlight, this function
-enables transient map with `set-transient-map'. You don't have to
-press the keybinding prefix again to move further to the next.
-That is, you can do a key sequence like this:
-
-   `\\[org-marginalia-next]' \] \] \] \]
-
-If you have the same prefix for `org-marginalia-prev', you can combine it in
-the sequence like so:
-
-   `\\[org-marginalia-next]' \] \] \[ \["
-  (interactive)
-  (if (not org-marginalia-highlights)
-      (progn (message "No highlights present in this buffer.") nil)
-    (let ((p (org-marginalia-find-next-highlight)))
-      (if p (progn
-              (goto-char p)
-              ;; Setup the overriding keymap.
-              (unless overriding-terminal-local-map
-                (let ((prefix-keys (substring (this-single-command-keys) 0 -1))
-                      (map (cdr org-marginalia-mode-map)))
-                  (when (< 0 (length prefix-keys))
-                    (mapc (lambda (k) (setq map (assq k map))) prefix-keys)
-                    (setq map (cdr-safe map))
-                    (when (keymapp map) (set-transient-map map t)))))
-              t)
-        (message "Nothing done. No more visible highlights exist") nil))))
-
-(defun org-marginalia-prev ()
-  "Look at the current point, and move to the previous highlight, if any.
-If there is none above the point, but there is a highlight in the
-buffer, go back to the last one.
-
-If the point has moved to the previous highlight, this function
-enables transient map with `set-transient-map'. You don't have to
-press the keybinding prefix again to move further to the next.
-That is, you can do a key sequence like this:
-
-   `\\[org-marginalia-prev]' \[ \[ \[ \[
-
-If you have the same prefix for `org-marginalia-next', you can combine it in
-the sequence like so:
-
-   `\\[org-marginalia-prev]' \] \] \[ \["
-  (interactive)
-  (if (not org-marginalia-highlights)
-      (progn (message "No highlights present in this buffer.") nil)
-    (let ((p (org-marginalia-find-prev-highlight)))
-      (if p (progn
-              (goto-char p)
-              ;; Setup the overriding keymap.
-              (unless overriding-terminal-local-map
-                (let ((prefix-keys (substring (this-single-command-keys) 0 -1))
-                      (map (cdr org-marginalia-mode-map)))
-                  (when (< 0 (length prefix-keys))
-                    (mapc (lambda (k) (setq map (assq k map))) prefix-keys)
-                    (setq map (cdr-safe map))
-                    (when (keymapp map) (set-transient-map map t)))))
-              t)
-        (message "Nothing done. No more visible highlights exist") nil))))
-
-(defun org-marginalia-toggle ()
-  "Toggle showing/hiding of highlighters in current buffer.
-It only affects the display of the highlighters. The locations
-are still kept tracked; thus, upon buffer-save the correct
-locations are still recorded in the marginalia file."
-  (interactive)
-  (when-let ((highlights org-marginalia-highlights))
-    ;; Check the first highlight in the buffer
-    ;; If it's hidden, all hidden. Show them.
-    ;; If not, all shown. Hide them.
-    (if-let* ((beg (overlay-start (nth 0 highlights)))
-              (hidden-p (get-char-property beg 'org-marginalia-hidden)))
-        (org-marginalia-show)
-      (org-marginalia-hide))
-    t))
-
-;;;; Functions
-
-;;;;; Private
-
-(defun org-marginalia-save-single-highlight (highlight title source-path)
-  "Save a single HIGHLIGHT in the marginalia file with properties.
-The marginalia file is specified by SOURCE-PATH. If headline with
-the same ID already exists, update it based on the new highlight
-position and highlighted text as TITLE. If it is a new highlight,
-creat a new headline at the end of the buffer."
-  (let* ((beg (overlay-start highlight))
-         (end (overlay-end highlight))
-        (id (overlay-get highlight 'org-marginalia-id))
-         ;;`org-with-wide-buffer is a macro that should work for non-Org file'
-         (text (org-with-wide-buffer (buffer-substring-no-properties beg 
end))))
-    ;; TODO Want to add a check if save is applicable here.
-    (with-current-buffer (find-file-noselect org-marginalia-notes-file-path)
-      (org-with-wide-buffer
-       (let ((file-headline (org-find-property org-marginalia-prop-source-file 
source-path))
-             (id-headline (org-find-property org-marginalia-prop-id id)))
-         (unless file-headline
-           ;; If file-headline does not exist, create one at the bottom
-           (goto-char (point-max))
-           ;; Ensure to be in the beginning of line to add a new headline
-           (when (eolp) (open-line 1) (forward-line 1) (beginning-of-line))
-           (insert (concat "* " title "\n"))
-           (org-set-property org-marginalia-prop-source-file source-path))
-         (cond (id-headline
-                (goto-char id-headline)
-                ;; Update the existing headline and position properties
-                (org-edit-headline text)
-                (org-set-property org-marginalia-prop-source-beg 
(number-to-string beg))
-                (org-set-property org-marginalia-prop-source-end 
(number-to-string end)))
-               (t ;; No headline with the ID property. Create one
-                (when-let ((p (org-find-property 
org-marginalia-prop-source-file source-path)))
-                  (goto-char p))
-                (org-narrow-to-subtree)
-                (goto-char (point-max))
-                ;; Ensure to be in the beginning of line to add a new headline
-                (when (eolp) (open-line 1) (forward-line 1) 
(beginning-of-line))
-                ;; Create a headline
-                ;; Add a properties
-                (insert (concat "** " text "\n"))
-                (org-set-property org-marginalia-prop-id id)
-                (org-set-property org-marginalia-prop-source-beg 
(number-to-string beg))
-                (org-set-property org-marginalia-prop-source-end 
(number-to-string end))
-                (insert (concat "[[file:" source-path "]" "[" title "]]"))))))
-      (when (buffer-modified-p) (save-buffer) t))))
-
-(defun org-marginalia-list-highlights-positions (&optional reverse)
-  "Return list of beg points of highlights in this buffer.
-By default, the list is in ascending order.
-If REVERSE is non-nil, return list in the descending order.
-
-It also checks if the position is visible or not. Returns only
-visible ones.
-
-If none, return nil."
-  (when org-marginalia-highlights
-    (let ((list org-marginalia-highlights))
-      (setq list (mapcar
-                  (lambda (h)
-                    (let ((p (overlay-start h)))
-                      ;; Checking if the p is visible or not
-                      (if (or
-                           (> p (point-max))
-                           (< p (point-min))
-                           ;; When the highlight is wihtin a visible folded
-                           ;; area, this function returns 'outline
-                           (org-invisible-p p))
-                          nil p)))
-                  list))
-      (setq list (remove nil list))
-      (when list
-        (if reverse (reverse list) list)))))
-
-(defun org-marginalia-sort-highlights-list ()
-  "Utility function to sort `org-marginalia-sort-highlights'.
-It checks if there is any element exists for `org-marginalia-highlights'.
-Instead of receiving it as an arg, it assumes its existence. It
-also distructively updates `org-marginalia-highlights'.
-It returns t when sorting is done."
-  (when org-marginalia-highlights
-    (setq org-marginalia-highlights
-         (seq-sort-by (lambda (ov) (overlay-start ov))
-                      #'<
-                      org-marginalia-highlights))
-    t))
-
-(defun org-marginalia-find-next-highlight ()
-  "Return the beg point of the next highlight.
-Look through `org-marginalia-highlights' list."
-  (when-let ((points (org-marginalia-list-highlights-positions)))
-      ;; Find the first occurance of p > (point). If none, this means all the
-      ;; points occur before the current point. Take the first one. Assume
-      ;; `org-marginalia-highlights' is sorted in the ascending order (it is).
-    (seq-find (lambda (p) (> p (point))) points (nth 0 points))))
-
-(defun org-marginalia-find-prev-highlight ()
-  "Return the beg point of the previous highlight.
-Look through `org-marginalia-highlights' list (in descending order)."
-  (when-let ((points (org-marginalia-list-highlights-positions 'reverse)))
-      ;; Find the first occurance of p < (point). If none, this means all the
-      ;; points occur before the current point. Take the first one. Assume
-      ;; `org-marginalia-highlights' is sorted in the descending order .
-    (seq-find (lambda (p) (< p (point))) points (nth 0 points))))
-
-(defun org-marginalia-hide ()
-  "Hide highlighters.
-It will remove the font-lock-face of all the highlights, and add
-'org-marginalia-hidden property with value 't. It does not check the current
-hidden state, thus not interactive. Use `org-marginalia-toggle'
-command to manually toggle the show/hide state."
-  (when-let ((highlights org-marginalia-highlights))
-    (dolist (highlight highlights)
-        (overlay-put highlight 'face nil)
-        (overlay-put highlight 'org-marginalia-hidden t))
-    t))
-
-(defun org-marginalia-show ()
-  "Show highlighters.
-It adds the font-lock-face to all the highlighted text regions.
-It does not check the current hidden state, thus not interactive.
-Use `org-marginalia-toggle' command to manually toggle the show/hide
-state."
-  (when-let ((highlights org-marginalia-highlights))
-    (dolist (highlight highlights)
-        (overlay-put highlight 'org-marginalia-hidden nil)
-        (overlay-put highlight 'face 'org-marginalia-highlighter))
-    t))
-
-;;;; Footer
-
-(provide 'org-marginalia)
-
-;;; org-marginalia.el ends here
-
-;; Local Variables:
-;; coding: utf-8
-;; fill-column: 80
-;; require-final-newline: t
-;; sentence-end-double-space: nil
-;; eval: (setq-local org-marginalia-notes-file-path "README.org")
-;; End:
+;;; org-marginalia.el --- highlight & annotate       -*- lexical-binding: t; 
-*-
+
+;; Copyright (C) 2020 Noboru Ota
+
+;; Author: Noboru Ota <me@nobiot.com>
+;; URL: https://github.com/nobiot/org-marginalia
+;; Version: 0.0.5
+;; Last Modified: 2021-01-05
+;; Package-Requires: ((emacs "27.1") (org "9.4"))
+;; Keywords: org-mode, annotation, writing, note-taking, margin-notes
+
+;; 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 of the License, 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;; This package lets you write margin notes (marginalia) for any text file in
+;; a separate Org file.
+
+;;;; Installation
+
+;;;;; MELPA
+
+;; This package is not available on MELPA. Manual installation required.
+
+;;;;; Manual
+
+;; Install these required packages:
+
+;; Ensure to have Org Mode 9.4 or later (tested on 9.4).  This package uses
+;; `org-collect-keywords', which does not exist in an earlier version.
+
+;; Then put this file in your load-path, and put this in your init
+;; file:
+;; (require 'org-marginalia)
+
+;;;; Usage
+
+;; - `org-marginalia-mode' ::
+;; Org-marginalia is a local minor mode. Toggle it on/off with using
+;; `org-marginalia-mode'. On activating, it loads your saved highlighters from
+;; the marginalia file, and enables automatic saving of highlighters. The
+;; automatic saving is achieved via function `org-marginalia-save' added to
+;; `after-save-hook'.
+
+;; - `org-marginalia-mark' (C-c n m by default) ::
+;; Select a region of text, and call `org-marginalia-mark' (bound to C-c n m 
by default)
+;; to highlight the region. It will generate a new ID, and start tracking the
+;; location -- so you can edit text around the marked text. Do not copy and
+;; paste as it will disappear and it is a bit tricky to recover the
+;; highlighter. To create a new margin note entry in themarginalia file, save 
the buffer.
+
+;; - `org-marginalia-save' ::
+;; By default, Org-marginalia creates or updates the highlighter's location
+;; and text inside automatically in the marginalia file. You can manually call
+;; `org-marginalia-save' to manually do it (automatic process also call this 
command).
+
+;; - `org-marginalia-open' (C-c o by default) ::
+;; Move your cursor on the highlighted text, and call `org-marginalia-open' to 
open the
+;; relevant margin notes in a separate window. Your cursor should move to the
+;; marginalia buffer narrowed to the relevant margin notes entry. You can edit
+;; the margin notes as a normal Org file. Once you have done editing, you can
+;; simply save and close the buffer (kill or close the window) as per your
+;; normal workflow. Technically, the marginalia buffer is a cloned indirect
+;; buffer of the marginalia file.
+
+;; - `org-marginalia-load' ::
+;; This command open the marginalia file and load the saved highlights onto
+;; current buffer. If there is no margin notes for it, it will output a
+;; message in the echo. Highlights tracked locally by this packages cannot
+;; persist when you kill the buffer, or quit Emacs. When you re-launch Emacs,
+;; ensure to turn on `org-marginalia-mode' to load the highlights. Load is
+;; automatically done when you activate the minor mode.
+
+;; - `org-marginalia-remove' ::
+;; This command removes the highlight at point. It will remove the highlight,
+;; and remove the properties from the marginalia, but will keep the headline
+;; and notes in tact.
+;;
+;; You can pass a universal argument with
+;; \\[universal-argument] (ARG). If this is the case, the command
+;; additionally deletes the entire heading subtree, along with the
+;; notes you have written, for the highlight."
+
+;; - `org-marginalia-next' (C-c n ] by default) ::
+;; Move to the next highlight if any. If there is none below the cursor, and
+;; there is a highlight above, loop back to the top one.
+
+;; If the point has moved to the next highlight, this function enables
+;; transient map with `set-transient-map'. You don't have to press the
+;; keybinding prefix again to move further to the next. That is, you can do a
+;; key sequence like this (assuming `org-marginalia-next' is bound to C-c n):
+
+;;   C-c n ] ] ] ]
+
+;; If you have the same prefix for `org-marginalia-prev', you can combine it 
in the
+;; sequence like so:
+
+;;  C-c n ] ] [ [
+;;  This lets your cursor back to where you started (next next prev prev)
+
+;; - `org-marginalia-prev' (C-c n [ by default) :: Move to the previous 
highlight if any.
+;; If there is none above the cursor, and there is a highlight below, loop
+;; back to the bottom one. This function enables transient map. See 
`org-marginalia-next'
+;; for detail.
+
+;; - `org-marginalia-toggle' ::
+;; Toggle showing/hiding of highlighters in current buffer. It only affects
+;; the display of the highlighters. When hidden, highlights' locations are
+;; still kept tracked; thus, upon buffer-save the correct locations are still
+;; recorded in the marginalia file.
+
+;;;; Customizing
+
+;; - Highlighter face can be changed via `org-marginalia-highlighter'
+;; - Marginalia file is defined with `org-marginalia-notes-file-path'
+
+;;;; Known Limitations
+
+;; - Turning off minor mode does not turn off the highlighters
+;;   This should not do any harm, but if you are distracted, kill the buffer
+;;   (not revert) and visit it again. Toggling show/hide of highlighters is
+;;   something I - would like to add later.
+
+;; - Copy & pasting loses highlights
+;;   You could mqanually recover it by adjusting the properties in the
+;;   marginalia file.
+
+;;;; Credits
+
+;; To create this package, I was inspired by the following packages. I did not
+;; copy any part of them, but borrowed some ideas from them -- e.g. saving the
+;; margin notes in a separate file.
+
+;; - [[https://github.com/jkitchin/ov-highlight][ov-highlight]]
+;;   John Kitchin's (author of Org-ref). Great UX for markers with hydra.
+;;   Saves the marker info and comments directly within the Org file as Base64
+;;   encoded string. It uses overlays.
+
+;; - [[https://github.com/bastibe/annotate.el][Annotate.el]]
+;;   Bastian Bechtold's (author of Org-journal). Unique display of annotations
+;;   right next to (or on top of) the text. It seems to be designed for very
+;;   short annotations, and perhaps for code review (programming practice); I
+;;   have seen recent issues reported when used with variable-pitch fonts
+;;   (prose).
+
+;; - 
[[https://github.com/tkf/org-mode/blob/master/contrib/lisp/org-annotate-file.el][Org-annotate-file]]
+;;   Part of Org's contrib library. It seems to be designed to annotate a
+;;   whole file in a separate Org file, rather than specific text items
+
+;; - [[https://github.com/IdoMagal/ipa.el][InPlaceAnnotations (ipa-mode)]]
+;;   It looks similar to Annotate.el above
+
+;;; Code:
+
+;;;; Requirements
+
+(require 'org)
+(require 'org-id)
+(declare-function org-collect-keywords 'org)
+
+;;;; Customization
+
+(defgroup org-marginalia nil
+  "Write margin notes (marginalia) for any text file in a
+separate Org file"
+  :group 'org
+  :prefix "org-marginalia-"
+  :link '(url-link :tag "Github" "https://github.com/nobiot/org-marginalia";))
+
+(defface org-marginalia-highlighter
+  '((((class color) (min-colors 88) (background light))
+     :underline "#aecf90" :background "#ecf7ed")
+    (((class color) (min-colors 88) (background dark))
+     :underline "#00422a" :background "#001904")
+    (t
+     :inherit highlight))
+  "Face for highlighters."
+  :group 'org-marginalia)
+
+(defcustom org-marginalia-notes-file-path "marginalia.org"
+  "Specify the file path for the marginalia.org file.
+The default is \"./marginalia.org\", thus one marginalia file per directory.
+Ensure that it is an Org file."
+  :type 'string
+  :group 'org-marginalia)
+
+(defcustom org-marginalia-tracking-file
+  (locate-user-emacs-file ".org-marginalia-tracking" nil)
+  "File name where the files `org-marginalia' tracks is saved.
+When `org-marginalia-global-tracking-mode' is active, opening a file
+saved in `org-marginalia-tracking-file' automatically loads highlights."
+  :type 'file)
+
+;;;; Variables
+
+(defvar-local org-marginalia-loaded nil)
+
+(defvar-local org-marginalia-highlights '()
+  "Keep track of all the highlights.
+It is a local variable and is a list of multiple highlights.
+Each element is an overlay representing a highlighted text region.
+
+On save-buffer each highlight will be persisted in the marginalia file
+(defined by `org-marginalia-notes-file-path').")
+
+(defvar org-marginalia-last-notes-buffer nil
+  "Stores the cloned indirect buffer for the margin notes.
+It is meant to exist only one of these in each Emacs session.")
+
+(defvar org-marginalia-tracking-file-loaded nil)
+
+(defvar org-marginalia-files-tracked nil)
+
+;; Const for the names of properties in Org Mode
+(defconst org-marginalia-prop-id "marginalia-id")
+(defconst org-marginalia-prop-source-file "marginalia-source-file")
+(defconst org-marginalia-prop-source-beg "marginalia-source-beg")
+(defconst org-marginalia-prop-source-end "marginalia-source-end")
+
+;;;; Commands
+
+;;;###autoload
+(define-minor-mode org-marginalia-global-tracking-mode
+  "Global mode. When enabled, check files saved in
+`org-marginalia-tracking-file' and opening them automatically
+activates `org-marginalia-mode' locally for the file opened."
+  :init-value nil
+  :lighter " marginalia-tracking"
+  :global t
+  (cond
+   (org-marginalia-global-tracking-mode
+    ;; Activate
+    (when (and (not org-marginalia-tracking-file-loaded)
+              (file-exists-p org-marginalia-tracking-file))
+      (org-marginalia-tracking-load))
+    (add-hook 'find-file-hook #'org-marginalia-tracking-auto-on)
+    (add-hook 'kill-emacs-hook #'org-marginalia-tracking-save))
+   (t
+    ;; dactivate
+    (setq org-marginalia-files-tracked nil)
+    (setq org-marginalia-tracking-file-loaded nil)
+    (remove-hook 'find-file-hook #'org-marginalia-tracking-auto-on)
+    (remove-hook 'kill-emacs-hook #'org-marginalia-tracking-save))))
+
+(defun org-marginalia-tracking-auto-on ()
+  (when (and org-marginalia-files-tracked
+            (member (abbreviate-file-name (buffer-file-name))
+                    org-marginalia-files-tracked))
+    (org-marginalia-mode +1)))
+
+(defun org-marginalia-tracking-load ()
+  ".
+Each line. It loads regardless of `org-marginalia-tracking-file';
+if already loaded this function reloads."
+  (with-temp-buffer
+    (condition-case nil
+       (progn
+         (insert-file-contents org-marginalia-tracking-file)
+         (setq org-marginalia-files-tracked
+               (split-string (buffer-string) "\n"))
+          (setq org-marginalia-tracking-file-loaded t)))))
+
+(defun org-marginalia-tracking-save ()
+  "."
+  (interactive)
+  (when org-marginalia-files-tracked
+    (with-temp-file org-marginalia-tracking-file
+      (insert (mapconcat 'identity org-marginalia-files-tracked "\n")))))
+
+;;;###autoload
+(define-minor-mode org-marginalia-mode
+    "Highlight text, write margin notes for any text file in Org Mode.
+
+This command toggles Org-marginalia local minor mode. On
+activation, it loads your saved highlights from the marginalia
+file, and enables automatic saving of highlights.
+
+The automatic saving is achieved via function
+`org-marginalia-save' added to `after-save-hook'.
+
+Interactively with no argument, this command toggles the mode. A
+positive prefix argument enables the mode, any other prefix
+argument disables it. From Lisp, argument omitted or nil enables
+the mode, `toggle' toggles the state.
+
+\\{org-marginalia-mode-map}"
+    :init-value nil
+    :lighter " marginalia"
+    :global nil
+    :keymap (let ((map (make-sparse-keymap)))
+              map)
+    (cond
+     (org-marginalia-mode
+      ;; Activate
+      (org-marginalia-load)
+      (add-hook 'after-save-hook #'org-marginalia-save nil t))
+     (t
+      ;; Deactivate
+      (when org-marginalia-highlights
+       (dolist (highlight org-marginalia-highlights)
+         (delete-overlay highlight)))
+      (setq org-marginalia-highlights nil)
+      (setq org-marginalia-loaded nil)
+      (remove-hook 'after-save-hook #'org-marginalia-save t))))
+
+;;;###autoload
+(defun org-marginalia-mark (beg end &optional id)
+  "Highlight the selected region (BEG and END).
+When used interactively. it will generate a new ID, always
+assuming it is a new highlighted text region, and start tracking
+the higlight's location, so that you can edit the text around.
+
+It will not create a marginalia entry yet. Call `org-marginalia-save' to
+create a new entry (it is automatic with `after-save-hook').
+
+When this function is called from Elisp, ID can be optionally
+passed. If so, no new ID gets generated.
+
+Every highlighted texts in the local buffer is tracked by
+`org-marginalia-highlights' local variable. The highlght is sorted by the
+beginning point in the ascending; this is useful for `org-marginalia-next'
+and `org-marginalia-prev'."
+  (interactive "r")
+  ;; Ensure to turn on the local minor mode
+  (unless org-marginalia-mode (org-marginalia-mode +1))
+  ;; UUID is too long; does not have to be the full length
+  (when (not id) (setq id (substring (org-id-uuid) 0 8)))
+  ;; Add highlight to the text
+  (org-with-wide-buffer
+   (let ((ov (make-overlay beg end)))
+     (overlay-put ov 'face 'org-marginalia-highlighter)
+     (overlay-put ov 'org-marginalia-id id)
+     ;; Keep track in a local variable It's a list overlays, guranteed to
+     ;; contain only marginalia overlays.
+
+     ;; TODO Do we need to consider this for overlay?
+     ;; `set-marker-insertion-type' to
+     ;; set the type t is necessary to move the cursor in sync with the
+     ;; font-lock-face property of the text property.
+     (push ov org-marginalia-highlights)
+     ;; Adding overlay does not set the buffer modified.
+     ;; It's more fluid with save operation.
+     ;; You cannot use `undo' to undo highlighter.
+     (deactivate-mark)
+     (unless (buffer-modified-p) (set-buffer-modified-p t))))
+  (org-marginalia-sort-highlights-list))
+
+;;;###autoload
+(defun org-marginalia-load ()
+  "Open the marginalia file and load the saved highlights onto current buffer.
+If there is no margin notes for it, it will output a message in
+the echo.
+
+Highlights tracked locally by this packages cannot persist when
+you kill the buffer, or quit Emacs. When you re-launch Emacs,
+ensure to turn on `org-marginalia-mode' to load the highlights.
+Load is automatically done when you activate the minor mode."
+  (interactive)
+  ;; Open the marginalia file
+  ;; Read all the positions
+  (unless org-marginalia-mode (org-marginalia-mode +1))
+  (unless org-marginalia-loaded
+    (when-let* ((filename (buffer-file-name))
+               (margin-buf (find-file-noselect org-marginalia-notes-file-path))
+               (source-path (abbreviate-file-name filename)))
+      ;; Get hilights: each highlighlight is stored as an alist
+      ;; (id beg . end)
+      ;; TODO check if there is any relevant notes for the current file
+      (let ((highlights '()))
+       (with-current-buffer margin-buf
+          (org-with-wide-buffer
+           (let ((heading (org-find-property
+                          org-marginalia-prop-source-file source-path)))
+             (if (not heading)
+                (message "No marginalia written for %s." source-path)
+               (goto-char (org-find-property
+                          org-marginalia-prop-source-file source-path))
+               ;; Narrow to only subtree for a single file
+               ;; `org-find-property' ensures that it is the beginning of H1
+               (org-narrow-to-subtree)
+               ;; It's important that the headline levels are fixed
+               ;; H1: File
+               ;; H2: Higlighted region (each one has a dedicated H2 subtree)
+               (while (not (org-next-visible-heading 1))
+                (when-let ((id (org-entry-get (point) "marginalia-id"))
+                            (beg (string-to-number
+                                 (org-entry-get (point)
+                                                "marginalia-source-beg")))
+                            (end (string-to-number
+                                 (org-entry-get (point)
+                                                "marginalia-source-end"))))
+                   (push (cons id (cons beg end)) highlights)))))))
+       ;; Back to the current buffer
+       ;; Look highilights and add highlights to the current buffer
+       (dolist (highlight highlights)
+          (let ((id (car highlight))
+               (beg (car (cdr highlight)))
+               (end (cdr (cdr highlight))))
+            (org-marginalia-mark beg end id)))))
+    (setq org-marginalia-loaded t)))
+
+(defun org-marginalia-save ()
+  "Save all the highlights tracked in current buffer to marginalia file.
+The marginalia file is defined in `org-marginalia-notes-file-path' variable.
+
+This funcion is automatically called when you save the buffer. This is
+achieved via `after-save-hook' (added via `org-marginalia-mode' when you
+activate the minor mode).
+
+`org-marginalia-highlights' is the local variable that tracks every highlight
+in the current buffer. Each highlight is represented by this data structure:
+
+   (id beg-marker . end-marker)"
+  (interactive)
+  (let* ((filename (buffer-file-name))
+         (source-path (abbreviate-file-name filename))
+         (title (or (car (cdr (assoc "TITLE" (org-collect-keywords 
'("TITLE")))))
+                    (file-name-sans-extension (file-name-nondirectory 
(buffer-file-name))))))
+    (dolist (highlight org-marginalia-highlights)
+      (org-marginalia-save-single-highlight highlight title source-path))
+    ;; Tracking
+    (when org-marginalia-files-tracked
+      (add-to-list 'org-marginalia-files-tracked (abbreviate-file-name 
(buffer-file-name))))))
+
+(defun org-marginalia-open (point)
+  "Open the margin notes at POINT, narrowed to the relevant headline.
+It creates a cloned indirect buffer of the marginalia file
+\(`org-marginalia-notes-file-path'\). You can edit the margin notes as a
+normal Org file. Once you have done editing, you can simply save and close the
+buffer (kill or close the window) as per your normal workflow.
+
+This package ensures that there is only one cloned buffer for marginalia by
+tracking it."
+  (interactive "d")
+  (when (buffer-live-p org-marginalia-last-notes-buffer)
+    (kill-buffer org-marginalia-last-notes-buffer))
+  (when-let ((id (get-char-property point 'org-marginalia-id))
+             (ibuf (make-indirect-buffer
+                   (find-file-noselect org-marginalia-notes-file-path) 
"*marginalia*" 'clone)))
+    (setq org-marginalia-last-notes-buffer ibuf)
+    (org-switch-to-buffer-other-window ibuf)
+    (widen)(goto-char (point-min))
+    (when (org-find-property org-marginalia-prop-id id)
+      (goto-char (org-find-property org-marginalia-prop-id id))
+      (org-narrow-to-subtree))))
+
+(defun org-marginalia-remove (point &optional arg)
+  "Remove the highlight at POINT.
+It will remove the highlight, and remove the properties from the
+marginalia, but will keep the headline and notes.
+
+You can pass a universal argument with
+\\[universal-argument] (ARG). If this is the case, the command
+additionally deletes the entire heading subtree, along with the
+notes you have written, for the highlight."
+  (interactive "d\nP")
+  ;; TODO There may be multple overlays
+  (when-let* ((id (get-char-property point 'org-marginalia-id)))
+    ;; Remove the highlight overlay and id
+    (dolist (ov (overlays-at (point)))
+      (when (overlay-get ov 'org-marginalia-id)
+       (delete ov org-marginalia-highlights)
+       (delete-overlay ov)))
+    ;; Remove the element in the variable org-marginalia-highlights
+    ;; TODO need to go through this org-marginalia-hightlights stuff
+    (org-marginalia-sort-highlights-list)
+    ;; Update the marginalia note file accordingly
+    (with-current-buffer (find-file-noselect org-marginalia-notes-file-path)
+      (org-with-wide-buffer
+       (when-let ((id-headline (org-find-property org-marginalia-prop-id id)))
+         (goto-char id-headline)
+        (org-narrow-to-subtree)
+         (org-delete-property org-marginalia-prop-id)
+         (org-delete-property org-marginalia-prop-source-beg)
+         (org-delete-property org-marginalia-prop-source-end)
+         (when arg
+           ;; TODO I would love to add the y-n prompt if there is any notes 
written
+           (delete-region (point-min)(point-max))
+           (message "Deleted the marginal notes.")))))
+    t))
+
+(defun org-marginalia-next ()
+  "Look at the current point, and move to the next highlight, if any.
+If there is none below the point, but there is a highlight in the
+buffer, go back to the first one.
+
+If the point has moved to the next highlight, this function
+enables transient map with `set-transient-map'. You don't have to
+press the keybinding prefix again to move further to the next.
+That is, you can do a key sequence like this:
+
+   `\\[org-marginalia-next]' \] \] \] \]
+
+If you have the same prefix for `org-marginalia-prev', you can combine it in
+the sequence like so:
+
+   `\\[org-marginalia-next]' \] \] \[ \["
+  (interactive)
+  (if (not org-marginalia-highlights)
+      (progn (message "No highlights present in this buffer.") nil)
+    (let ((p (org-marginalia-find-next-highlight)))
+      (if p (progn
+              (goto-char p)
+              ;; Setup the overriding keymap.
+              (unless overriding-terminal-local-map
+                (let ((prefix-keys (substring (this-single-command-keys) 0 -1))
+                      (map (cdr org-marginalia-mode-map)))
+                  (when (< 0 (length prefix-keys))
+                    (mapc (lambda (k) (setq map (assq k map))) prefix-keys)
+                    (setq map (cdr-safe map))
+                    (when (keymapp map) (set-transient-map map t)))))
+              t)
+        (message "Nothing done. No more visible highlights exist") nil))))
+
+(defun org-marginalia-prev ()
+  "Look at the current point, and move to the previous highlight, if any.
+If there is none above the point, but there is a highlight in the
+buffer, go back to the last one.
+
+If the point has moved to the previous highlight, this function
+enables transient map with `set-transient-map'. You don't have to
+press the keybinding prefix again to move further to the next.
+That is, you can do a key sequence like this:
+
+   `\\[org-marginalia-prev]' \[ \[ \[ \[
+
+If you have the same prefix for `org-marginalia-next', you can combine it in
+the sequence like so:
+
+   `\\[org-marginalia-prev]' \] \] \[ \["
+  (interactive)
+  (if (not org-marginalia-highlights)
+      (progn (message "No highlights present in this buffer.") nil)
+    (let ((p (org-marginalia-find-prev-highlight)))
+      (if p (progn
+              (goto-char p)
+              ;; Setup the overriding keymap.
+              (unless overriding-terminal-local-map
+                (let ((prefix-keys (substring (this-single-command-keys) 0 -1))
+                      (map (cdr org-marginalia-mode-map)))
+                  (when (< 0 (length prefix-keys))
+                    (mapc (lambda (k) (setq map (assq k map))) prefix-keys)
+                    (setq map (cdr-safe map))
+                    (when (keymapp map) (set-transient-map map t)))))
+              t)
+        (message "Nothing done. No more visible highlights exist") nil))))
+
+(defun org-marginalia-toggle ()
+  "Toggle showing/hiding of highlighters in current buffer.
+It only affects the display of the highlighters. The locations
+are still kept tracked; thus, upon buffer-save the correct
+locations are still recorded in the marginalia file."
+  (interactive)
+  (when-let ((highlights org-marginalia-highlights))
+    ;; Check the first highlight in the buffer
+    ;; If it's hidden, all hidden. Show them.
+    ;; If not, all shown. Hide them.
+    (if-let* ((beg (overlay-start (nth 0 highlights)))
+              (hidden-p (get-char-property beg 'org-marginalia-hidden)))
+        (org-marginalia-show)
+      (org-marginalia-hide))
+    t))
+
+;;;; Functions
+
+;;;;; Private
+
+(defun org-marginalia-save-single-highlight (highlight title source-path)
+  "Save a single HIGHLIGHT in the marginalia file with properties.
+The marginalia file is specified by SOURCE-PATH. If headline with
+the same ID already exists, update it based on the new highlight
+position and highlighted text as TITLE. If it is a new highlight,
+creat a new headline at the end of the buffer."
+  (let* ((beg (overlay-start highlight))
+         (end (overlay-end highlight))
+        (id (overlay-get highlight 'org-marginalia-id))
+         ;;`org-with-wide-buffer is a macro that should work for non-Org file'
+         (text (org-with-wide-buffer (buffer-substring-no-properties beg 
end))))
+    ;; TODO Want to add a check if save is applicable here.
+    (with-current-buffer (find-file-noselect org-marginalia-notes-file-path)
+      (org-with-wide-buffer
+       (let ((file-headline (org-find-property org-marginalia-prop-source-file 
source-path))
+             (id-headline (org-find-property org-marginalia-prop-id id)))
+         (unless file-headline
+           ;; If file-headline does not exist, create one at the bottom
+           (goto-char (point-max))
+           ;; Ensure to be in the beginning of line to add a new headline
+           (when (eolp) (open-line 1) (forward-line 1) (beginning-of-line))
+           (insert (concat "* " title "\n"))
+           (org-set-property org-marginalia-prop-source-file source-path))
+         (cond (id-headline
+                (goto-char id-headline)
+                ;; Update the existing headline and position properties
+                (org-edit-headline text)
+                (org-set-property org-marginalia-prop-source-beg 
(number-to-string beg))
+                (org-set-property org-marginalia-prop-source-end 
(number-to-string end)))
+               (t ;; No headline with the ID property. Create one
+                (when-let ((p (org-find-property 
org-marginalia-prop-source-file source-path)))
+                  (goto-char p))
+                (org-narrow-to-subtree)
+                (goto-char (point-max))
+                ;; Ensure to be in the beginning of line to add a new headline
+                (when (eolp) (open-line 1) (forward-line 1) 
(beginning-of-line))
+                ;; Create a headline
+                ;; Add a properties
+                (insert (concat "** " text "\n"))
+                (org-set-property org-marginalia-prop-id id)
+                (org-set-property org-marginalia-prop-source-beg 
(number-to-string beg))
+                (org-set-property org-marginalia-prop-source-end 
(number-to-string end))
+                (insert (concat "[[file:" source-path "]" "[" title "]]"))))))
+      (when (buffer-modified-p) (save-buffer) t))))
+
+(defun org-marginalia-list-highlights-positions (&optional reverse)
+  "Return list of beg points of highlights in this buffer.
+By default, the list is in ascending order.
+If REVERSE is non-nil, return list in the descending order.
+
+It also checks if the position is visible or not. Returns only
+visible ones.
+
+If none, return nil."
+  (when org-marginalia-highlights
+    (let ((list org-marginalia-highlights))
+      (setq list (mapcar
+                  (lambda (h)
+                    (let ((p (overlay-start h)))
+                      ;; Checking if the p is visible or not
+                      (if (or
+                           (> p (point-max))
+                           (< p (point-min))
+                           ;; When the highlight is wihtin a visible folded
+                           ;; area, this function returns 'outline
+                           (org-invisible-p p))
+                          nil p)))
+                  list))
+      (setq list (remove nil list))
+      (when list
+        (if reverse (reverse list) list)))))
+
+(defun org-marginalia-sort-highlights-list ()
+  "Utility function to sort `org-marginalia-sort-highlights'.
+It checks if there is any element exists for `org-marginalia-highlights'.
+Instead of receiving it as an arg, it assumes its existence. It
+also distructively updates `org-marginalia-highlights'.
+It returns t when sorting is done."
+  (when org-marginalia-highlights
+    (setq org-marginalia-highlights
+         (seq-sort-by (lambda (ov) (overlay-start ov))
+                      #'<
+                      org-marginalia-highlights))
+    t))
+
+(defun org-marginalia-find-next-highlight ()
+  "Return the beg point of the next highlight.
+Look through `org-marginalia-highlights' list."
+  (when-let ((points (org-marginalia-list-highlights-positions)))
+      ;; Find the first occurance of p > (point). If none, this means all the
+      ;; points occur before the current point. Take the first one. Assume
+      ;; `org-marginalia-highlights' is sorted in the ascending order (it is).
+    (seq-find (lambda (p) (> p (point))) points (nth 0 points))))
+
+(defun org-marginalia-find-prev-highlight ()
+  "Return the beg point of the previous highlight.
+Look through `org-marginalia-highlights' list (in descending order)."
+  (when-let ((points (org-marginalia-list-highlights-positions 'reverse)))
+      ;; Find the first occurance of p < (point). If none, this means all the
+      ;; points occur before the current point. Take the first one. Assume
+      ;; `org-marginalia-highlights' is sorted in the descending order .
+    (seq-find (lambda (p) (< p (point))) points (nth 0 points))))
+
+(defun org-marginalia-hide ()
+  "Hide highlighters.
+It will remove the font-lock-face of all the highlights, and add
+'org-marginalia-hidden property with value 't. It does not check the current
+hidden state, thus not interactive. Use `org-marginalia-toggle'
+command to manually toggle the show/hide state."
+  (when-let ((highlights org-marginalia-highlights))
+    (dolist (highlight highlights)
+        (overlay-put highlight 'face nil)
+        (overlay-put highlight 'org-marginalia-hidden t))
+    t))
+
+(defun org-marginalia-show ()
+  "Show highlighters.
+It adds the font-lock-face to all the highlighted text regions.
+It does not check the current hidden state, thus not interactive.
+Use `org-marginalia-toggle' command to manually toggle the show/hide
+state."
+  (when-let ((highlights org-marginalia-highlights))
+    (dolist (highlight highlights)
+        (overlay-put highlight 'org-marginalia-hidden nil)
+        (overlay-put highlight 'face 'org-marginalia-highlighter))
+    t))
+
+;;;; Footer
+
+(provide 'org-marginalia)
+
+;;; org-marginalia.el ends here
+
+;; Local Variables:
+;; coding: utf-8
+;; fill-column: 80
+;; require-final-newline: t
+;; sentence-end-double-space: nil
+;; eval: (setq-local org-marginalia-notes-file-path "README.org")
+;; End: