#+title: denote-org: Extensions to better integrate Org with Denote
#+author: Protesilaos Stavrou
#+email: info@protesilaos.com
#+language: en
#+options: ':t toc:nil author:t email:t num:t
#+startup: content
#+macro: stable-version 0.2.0
#+macro: release-date 2025-10-17
#+macro: development-version 0.3.0-dev
#+export_file_name: denote-org.texi
#+texinfo_filename: denote-org.info
#+texinfo_dir_category: Emacs misc features
#+texinfo_dir_title: Denote Org: (denote-org)
#+texinfo_dir_desc: Extensions to better integrate Org with Denote
#+texinfo_header: @set MAINTAINERSITE @uref{https://protesilaos.com,maintainer webpage}
#+texinfo_header: @set MAINTAINER Protesilaos Stavrou
#+texinfo_header: @set MAINTAINEREMAIL @email{info@protesilaos.com}
#+texinfo_header: @set MAINTAINERCONTACT @uref{mailto:info@protesilaos.com,contact the maintainer}

#+texinfo: @insertcopying

This manual, written by Protesilaos Stavrou, describes the customization
options for the Emacs package called ~denote~ (or =denote.el=), and
provides every other piece of information pertinent to it.

The documentation furnished herein corresponds to stable version
{{{stable-version}}}, released on {{{release-date}}}.  Any reference to
a newer feature which does not yet form part of the latest tagged
commit, is explicitly marked as such.

Current development target is {{{development-version}}}.

+ Package name (GNU ELPA): ~denote-org~
+ Official manual: <https://protesilaos.com/emacs/denote-org>
+ Git repository: <https://github.com/protesilaos/denote-org>
+ Backronym: Denote... Ordinarily Restricts Gyrations.

If you are viewing the README.org version of this file, please note that
the GNU ELPA machinery automatically generates an Info manual out of it.

#+toc: headlines 8 insert TOC here, with eight headline levels

* COPYING
:PROPERTIES:
:COPYING: t
:CUSTOM_ID: h:copying
:END:

Copyright (C) 2022-2025  Free Software Foundation, Inc.

#+begin_quote
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or
any later version published by the Free Software Foundation; with no
Invariant Sections, with the Front-Cover Texts being “A GNU Manual,” and
with the Back-Cover Texts as in (a) below.  A copy of the license is
included in the section entitled “GNU Free Documentation License.”

(a) The FSF’s Back-Cover Text is: “You have the freedom to copy and
modify this GNU manual.”
#+end_quote

* Overview
:PROPERTIES:
:CUSTOM_ID: h:6157c29a-31e6-4ba7-b114-57f94a21d460
:END:

The ~denote-org~ package contains extra features that better integrate
Denote with Org mode. These used to be available as part of the main
~denote~ package in a file called =denote-org-extras.el=, but now live
in this standalone package to main things easier to maintain and
understand.

With ~denote-org~, users have Org-specific extensions such as dynamic
blocks, links to headings, and splitting an Org subtree into its own
standalone file. The following sections cover the technicalities.

* Use Org dynamic blocks
:PROPERTIES:
:CUSTOM_ID: h:8b542c50-dcc9-4bca-8037-a36599b22779
:END:

Denote can optionally integrate with Org mode's "dynamic blocks"
facility. This means that it can use special blocks that are evaluated
with =C-c C-x C-u= (~org-dblock-update~) to generate their contents.
The following subsections describe the types of Org dynamic blocks
provided by Denote.

- [[#h:50160fae-6515-4d7d-9737-995ad925e64b][Org dynamic blocks to insert links or backlinks]]
- [[#h:f15fa143-5036-416f-9bff-1bcabbb03456][Org dynamic block to insert file contents]]

A dynamic block gets its contents by evaluating a function that
corresponds to the type of block. The block type and its parameters
are stated in the opening =#+BEGIN= line. Typing =C-c C-x C-u=
(~org-dblock-update~) with point on that line runs (or re-runs) the
associated function with the given parameters and populates the
block's contents accordingly.

Dynamic blocks are particularly useful for metanote entries that
reflect on the status of earlier notes (read the Denote manual's
section about writing metanotes).

The Org manual describes the technicalities of Dynamic Blocks.
Evaluate:

#+begin_src emacs-lisp
(info "(org) Dynamic Blocks")
#+end_src

The ~org-dynamic-block-insert-dblock~ function (=C-c C-x x=) provides a dropdown menu of all available dynamic blocks.

** Org dynamic blocks to insert links
:PROPERTIES:
:CUSTOM_ID: h:50160fae-6515-4d7d-9737-995ad925e64b
:END:

#+findex: denote-org-dblock-insert-links
The =denote-links= block can be inserted at point with the command
~denote-org-dblock-insert-links~ or by manually including the
following in an Org file:

: #+BEGIN: denote-links :regexp "YOUR REGEXP HERE" :not-regexp nil :excluded-dirs-regexp nil :sort-by-component nil :reverse-sort nil :id-only nil :include-date nil
:
: #+END:

All the parameters except for =:regexp= are optional.

The =denote-links= block is also registered as an option for the
command ~org-dynamic-block-insert-dblock~.

Type =C-c C-x C-u= (~org-dblock-update~) with point on the =#+BEGIN=
line to update the block.

- The =:regexp= parameter is mandatory. Its value is a string and its
  behaviour is the same as that of the standard ~denote-add-links~
  command (part of the main ~denote~ package). Concretely, it produces
  a typographic list of links to files matching the giving regular
  expression. The value of the =:regexp= parameter may also be of the
  form read by the ~rx~ macro (Lisp notation instead of a string), as
  explained in the Emacs Lisp Reference Manual (evaluate this code to
  read the documentation: =(info "(elisp) Rx Notation")=). Note that
  you do not need to write an actual regular expression to get
  meaningful results: even something like =_journal= will work to
  include all files that have a =journal= keyword.

- The =:not-regexp= parameter is optional. It is a regular expression
  that applies after =:regexp= to filter out the matching files.

- The =:excluded-dirs-regexp= is a string that contains a word or
  regular expression that matches against directory files names
  to-be-excluded from the results. This has the same meaning as
  setting the ~denote-excluded-directories-regexp~ user option (which
  is part of the main ~denote~ package). The user option has a global
  effect, which is overridden locally in the dynamic block. When the
  value of =:excluded-dirs-regexp= is nil (the default), the value of
  ~denote-excluded-directories-regexp~ is used (which is also nil by
  default, meaning that all directories are included). When the value
  of =excluded-dirs-regexp= is ~t~ or some other symbol, then the
  ~denote-excluded-directories-regexp~ is ignored altogether. This is
  useful in the scenario where the user option is set to exclude some
  directories but the dynamic blocks wants to lift that restriction.

- The =:sort-by-component= parameter is optional. It sorts the files
  by the given Denote file name component. The value it accepts is an
  unquoted symbol among =title=, =keywords=, =signature=,
  =identifier=, =random=, =last-modified=. When using the command
  ~denote-org-dblock-insert-files~, this parameter is automatically
  inserted together with the (=:regexp= parameter) and the user is
  prompted for a file name component.

- The =:reverse-sort= parameter is optional. It reverses the order in
  which files appear in. This is meaningful even without the presence
  of the parameter =:sort-by-component=, though it also combines with
  it.

- The =:id-only= parameter is optional. It accepts a ~t~ value, in
  which case links are inserted without a description text but only
  with the identifier of the given file. This has the same meaning as
  with the ~denote-link~ command and related facilities (read the
  Denote manual's section about linking to other files in the
  ~denote-directory~).

- The =:include-date= parameter controls whether to display the date
  of the file name after the title. This is done when its value is
  ~t~. By default (a nil value), no date is shown.

- An optional =:block-name= parameter can be specified with a string
  value to add a =#+name= to the results. This is useful for further
  processing using Org facilities (a feature that is outside Denote's
  purview).

In some workflows, users may want to have a separate block to see what
other links they are missing since they last updated the dynamic
block. We cover that case as well ([[#h:1a81e255-0510-4ee0-bc3a-374de048ef46][The Org dynamic block to insert missing links only]]).

** The Org dynamic block to insert missing links only
:PROPERTIES:
:CUSTOM_ID: h:1a81e255-0510-4ee0-bc3a-374de048ef46
:END:

#+findex: denote-org-dblock-insert-missing-links
The =denote-missing-links= block is available with the command
~denote-org-dblock-insert-missing-links~. It is like the
aforementioned =denote-links= block, except it only lists links to
files that are not present in the current buffer ([[#h:50160fae-6515-4d7d-9737-995ad925e64b][Org dynamic blocks to insert links]]).
The parameters are otherwise the same and are all optional except for
=:regexp=:

: #+BEGIN: denote-missing-links :regexp "YOUR REGEXP HERE" :not-regexp nil :excluded-dirs-regexp nil :sort-by-component nil :reverse-sort nil :id-only nil :include-date nil
:
: #+END:

The =denote-missing-links= block is also registered as an option for the
command ~org-dynamic-block-insert-dblock~.

Remember to type =C-c C-x C-u= (~org-dblock-update~) with point on the
=#+BEGIN= line to update the block.

** The Org dynamic block to insert backlinks
:PROPERTIES:
:CUSTOM_ID: h:f9a97859-1deb-47dd-bdae-52f8b424ff46
:END:

#+findex: denote-org-dblock-insert-backlinks
Apart from links to files matching a regular expression, we can also
produce a list of backlinks to the current file. The dynamic block can
be inserted at point with the command ~denote-org-dblock-insert-backlinks~
or by manually writing this in an Org file:

: #+BEGIN: denote-backlinks :not-regexp nil :excluded-dirs-regexp nil :sort-by-component nil :reverse-sort nil :id-only nil :this-heading-only nil :include-date nil
:
: #+END:

The =denote-backlinks= block is also registered as an option for the
command ~org-dynamic-block-insert-dblock~.

Remember to type =C-c C-x C-u= (~org-dblock-update~) with point on the
=#+BEGIN= line to update the block.

The parameters recognised by this dynamic block are almost the same as
that for inserting links ([[#h:50160fae-6515-4d7d-9737-995ad925e64b][Org dynamic blocks to insert links]]). They
are all optional in this case and there is no parameter expecting a
regular expression for matching files to link to.

Additionally, the ~denote-backlinks~ block also recognises the
=:this-heading-only= parameter. It determines if the backlinks are
about the file or the heading under which the dynamic block is inserted
([[#h:604bf92a-908a-485c-98b8-37ccae559afd][Backlinks for Org headings]]). When this parameter is omitted or nil
(the default), then the backlinks are about the whole file, but if
this parameter has a ~t~ value then the backlinks are specifically for
the heading ([[#h:fc1ad245-ec08-41be-8d1e-7153d99daf02][Insert link to an Org file with a further pointer to a heading]]).

** Org dynamic block to insert file contents
:PROPERTIES:
:CUSTOM_ID: h:f15fa143-5036-416f-9bff-1bcabbb03456
:END:

Denote can optionally use Org's dynamic blocks facility to produce a
section that lists entire file contents ([[#h:8b542c50-dcc9-4bca-8037-a36599b22779][Use Org dynamic blocks]]).
This works by instructing Org to match a regular expression of Denote
files, the same way we do with Denote links (read the Denote manual's
section about inserting links that match a regular expression).

This is useful to, for example, compile a dynamically concatenated
list of scattered thoughts on a given topic, like =^2023.*_emacs= for
a long entry that incorporates all the notes written in 2023 with the
keyword =emacs=.

#+findex: denote-org-dblock-insert-files
To produce such a block, call the command ~denote-org-dblock-insert-files~
or manually write the following block in an Org file and then type
 =C-c C-x C-u= (~org-dblock-update~) on the =#+BEGIN= line to run it
(do it again to recalculate the block):

: #+BEGIN: denote-files :regexp "YOUR REGEXP HERE" :not-regexp nil :sort-by-component nil :reverse-sort nil :no-front-matter nil :file-separator nil :add-links nil
:
: #+END:

All parameters are optional except for =:regexp=.

The =denote-files= block is also registered as an option for the
command ~org-dynamic-block-insert-dblock~.

Remember to type =C-c C-x C-u= (~org-dblock-update~) with point on the
=#+BEGIN= line to update the block.

To fully control the output, include these additional optional
parameters, which are described further below:

- The =:regexp= parameter is mandatory. Its value is a string,
  representing a regular expression to match Denote file names. Its
  value may also be an ~rx~ expression instead of a string, as noted
  in the previous section ([[#h:50160fae-6515-4d7d-9737-995ad925e64b][Org dynamic blocks to insert links or backlinks]]).
  Note that you do not need to write an actual regular expression to
  get meaningful results: even something like =_journal= will work to
  include all files that have a =journal= keyword.

- The =:not-regexp= parameter is optional. It is a regular expression
  that applies after =:regexp= to filter out the matching files.

- The =:excluded-dirs-regexp= is a string that contains a word or
  regular expression that matches against directory files names
  to-be-excluded from the results. This has the same meaning as
  setting the ~denote-excluded-directories-regexp~ user option (which
  is part of the main ~denote~ package). The user option has a global
  effect, which is overridden locally in the dynamic block. When the
  value of =:excluded-dirs-regexp= is nil (the default), the value of
  ~denote-excluded-directories-regexp~ is used (which is also nil by
  default, meaning that all directories are included). When the value
  of =excluded-dirs-regexp= is ~t~ or some other symbol, then the
  ~denote-excluded-directories-regexp~ is ignored altogether. This is
  useful in the scenario where the user option is set to exclude some
  directories but the dynamic blocks wants to lift that restriction.

- The =:sort-by-component= parameter is optional. It sorts the files
  by the given Denote file name component. The value it accepts is an
  unquoted symbol among =title=, =keywords=, =signature=,
  =identifier=, =random=, =last-modified=. When using the command
  ~denote-org-dblock-insert-files~, this parameter is automatically
  inserted together with the (=:regexp= parameter) and the user is
  prompted for a file name component.

- The =:reverse-sort= parameter is optional. It reverses the order in
  which files appear in. This is meaningful even without the presence
  of the parameter =:sort-by-component=, though it also combines with
  it.

#+vindex: denote-org-dblock-file-contents-separator
- The =:file-separator= parameter is optional. If it is omitted, then
  Denote will use no separator between the files it inserts. If the
  value is ~t~ the ~denote-org-dblock-file-contents-separator~ is
  applied at the end of each file: it introduces some empty lines and
  a horizontal rule between them to visually distinguish individual
  files. If the =:file-separator= value is a string, it is used as the
  file separator (e.g. use ="\n"= to insert just one empty new line).

- The =:no-front-matter= parameter is optional. When set to a ~t~
  value, Denote tries to remove front matter from the files it is
  inserting in the dynamic block. The technique used to perform this
  operation is by removing all lines from the top of the file until
  the first empty line. This works with the default front matter that
  Denote adds, but is not 100% reliable with all sorts of user-level
  modifications and edits to the file. When the =:no-front-matter= is
  set to a natural number, Denote will omit that many lines from the
  top of the file.

- The =:add-links= parameter is optional. When it is set to a ~t~
  value, all files are inserted as a typographic list and are indented
  accordingly. The first line in each list item is a link to the file
  whose contents are inserted in the following lines. When the value
  is =id-only=, then links are inserted without a description text but
  only with the identifier of the given file. This has the same
  meaning as with the ~denote-link~ command and related facilities
  (those are explained at length in the Denote manual). Remember that
  Org can fold the items in a typographic list the same way it does
  with headings. So even long files can be presented in this format
  without much trouble.

- An optional =:block-name= parameter can be specified with a string
  value to add a =#+name= to the results. This is useful for further
  processing using Org facilities (a feature that is outside Denote's
  purview).

** Org dynamic block to insert Org files as headings
:PROPERTIES:
:CUSTOM_ID: h:d6254a12-b762-4096-a5de-66a0d423e204
:END:

[ IMPORTANT NOTE: This dynamic block only works with Org files,
  because it has to assume the Org notation in order to insert each
  file's contents as its own heading. ]

#+findex: denote-org-dblock-insert-files-as-headings
As a variation of the previously covered block that inserts file
contents, we have the ~denote-org-dblock-insert-files-as-headings~
command ([[#h:f15fa143-5036-416f-9bff-1bcabbb03456][Org dynamic block to insert file contents]]). It Turn the
=#+title= of each file into a top-level heading. Then it increments
all original headings in the file by one, so that they become
subheadings of what once was the =#+title=. Similarly, the
=#+filetags= of each file as tags for the top-level heading
(what was the =#+title=).

Because of how it is meant to work, this dynamic block only works with
Org files.

In its simplest form, this dynamic block looks like this, with
=:regexp= as the only mandatory parameter:

: #+BEGIN: denote-files-as-headings :regexp "YOUR REGEXP HERE"
:
: #+END:

Though when you use the command ~denote-org-dblock-insert-files-as-headings~
you get all the parameters included:

: #+BEGIN: denote-files-as-headings :regexp "YOUR REGEXP HERE" :not-regexp nil :excluded-dirs-regexp nil :sort-by-component title :reverse-sort nil :add-links nil :exclude-tags nil
:
: #+END:

- The =:regexp= parameter is mandatory. Its value is a string,
  representing a regular expression to match Denote file names. Its
  value may also be an ~rx~ expression instead of a string, as noted
  in the previous section ([[#h:50160fae-6515-4d7d-9737-995ad925e64b][Org dynamic blocks to insert links or backlinks]]).
  Note that you do not need to write an actual regular expression to
  get meaningful results: even something like =_journal= will work to
  include all files that have a =journal= keyword.

- The =:not-regexp= parameter is optional. It is a regular expression
  that applies after =:regexp= to filter out the matching files.

- The =:excluded-dirs-regexp= is a string that contains a word or
  regular expression that matches against directory files names
  to-be-excluded from the results. This has the same meaning as
  setting the ~denote-excluded-directories-regexp~ user option (which
  is part of the main ~denote~ package)). The user option has a global
  effect, which is overridden locally in the dynamic block. When the
  value of =:excluded-dirs-regexp= is nil (the default), the value of
  ~denote-excluded-directories-regexp~ is used (which is also nil by
  default, meaning that all directories are included). When the value
  of =excluded-dirs-regexp= is ~t~ or some other symbol, then the
  ~denote-excluded-directories-regexp~ is ignored altogether. This is
  useful in the scenario where the user option is set to exclude some
  directories but the dynamic blocks wants to lift that restriction.

- The =:sort-by-component= parameter is optional. It sorts the files
  by the given Denote file name component. The value it accepts is an
  unquoted symbol among =title=, =keywords=, =signature=,
  =identifier=, =random=, =last-modified=. When using the command
  ~denote-org-dblock-insert-files~, this parameter is automatically
  inserted together with the (=:regexp= parameter) and the user is
  prompted for a file name component.

- The =:reverse-sort= parameter is optional. It reverses the order in
  which files appear in. This is meaningful even without the presence
  of the parameter =:sort-by-component=, though it also combines with
  it.

- The =:add-links= parameter is optional. When it is set to a ~t~
  value, all the top-level headings (those that were the =#+title= of
  each file) are generated as links, pointing to the original file.
  This has the same meaning as with the ~denote-link~ command and
  related facilities (those are explained at length in the Denote manual).

- The =:exclude-tags= parameter is optional. It controls whether the
  =#+filetags= of the matching file are appended to the title as tags.
  This is what happens by default. If =:exclude-tags= is non-nil, then
  the tags are omitted.

- An optional =:block-name= parameter can be specified with a string
  value to add a =#+name= to the results. This is useful for further
  processing using Org facilities (a feature that is outside Denote's
  purview).

** Org dynamic block to insert sequences
:PROPERTIES:
:CUSTOM_ID: h:4ba84125-3ec4-4feb-926e-3aae91d0844e
:END:

#+findex: denote-org-dblock-insert-sequence
The Denote-Sequence package enables using the Denote signature as a
hierarchical indicator inspired by the Folgezettel principle in the
Zettelkasten methodology.

The =denote-sequence= block can be inserted at point with the command
~denote-org-dblock-insert-sequence~ or by manually including the
following in an Org file:

: #+BEGIN: denote-sequence :sequence "1=1" :depth 2
:
: #+END:

The =:sequence= is required, while =:depth= is optional.

- The sequence is the root of the hierarchy displayed in the dynamic
  block. It consists of the text of the sequence, whose numeric format
  is like ~1=1~ or, for its alphanumeric counterpart, =1a=.

  A value of =:sequence= which is an empty string =""= or the regular
  expression for "match anything at least once", namely =".+"=, mean
  to collect all the sequences with their children.

- The depth is the relative depth from the root note: the number 2 is
  for the children of the given sequence, 3 for grandchildren, and so
  on. A value of ~nil~ means to find all descendants of the given
  sequence.

The list of links is indented to visualise their hierarchical structure.

* Create a note from the current Org subtree
:PROPERTIES:
:CUSTOM_ID: h:d0c7cb79-21e5-4176-a6af-f4f68578c8dd
:END:

In Org parlance, an entry with all its subheadings and other contents
is a "subtree". Denote can operate on the subtree to extract it from
the current file and create a new file out of it. One such workflow is
to collect thoughts in a single document and produce longer standalone
notes out of them upon review.

#+findex: denote-org-extract-org-subtree
The command ~denote-org-extract-org-subtree~ is used for this
purpose. It creates a new Denote note using the current Org subtree.
In doing so, it removes the subtree from its current file and moves
its contents into a new file. This command is part of the optional
=denote-org.el= extension, which is part of the ~denote~
package. It is loaded automatically as soon as one of its commands is
invoked.

The text of the subtree's heading becomes the =#+title= of the new
note. Everything else is inserted as-is.

If the heading has any tags, they are used as the keywords of the new
note. If the Org file has any =#+filetags= they are taken as well
(Org's =#+filetags= are inherited by the headings). If none of these
are true and the user option ~denote-prompts~ includes an entry for
keywords, then ~denote-org-extract-org-subtree~ prompts for
keywords. Else the new note has no keywords.

If the heading has a =PROPERTIES= drawer, it is retained for further
review.

If the heading's =PROPERTIES= drawer includes a =DATE= or =CREATED=
property, or there exists a =CLOSED= statement with a timestamp value,
use that to derive the date (or date and time) of the new note (if
there is only a date, the time is taken as 00:00). If more than one of
these is present, the order of preference is =DATE=, then =CREATED=,
then =CLOSED=. If none of these is present, the current time is used.
If the ~denote-prompts~ includes an entry for a date, then the command
prompts for a date at this stage (also see ~denote-date-prompt-use-org-read-date~).

For the rest, it consults the value of the user option
~denote-prompts~ in the following scenaria:

- To optionally prompt for a subdirectory, otherwise it produces the
  new note in the ~denote-directory~.
- To optionally prompt for a file signature, otherwise to not use any.

The new note is an Org file regardless of the user option
~denote-file-type~.

* Insert link to an Org file with a further pointer to a heading
:PROPERTIES:
:CUSTOM_ID: h:fc1ad245-ec08-41be-8d1e-7153d99daf02
:END:

#+findex: denote-org-link-to-heading
As part of the optional =denote-org.el= extension, the command
~denote-org-link-to-heading~ prompts for a link to an Org file
and then asks for a heading therein, using minibuffer completion. Once
the user provides input at the two prompts, the command inserts a link
at point which has the following pattern: =[[denote:IDENTIFIER::#ORG-HEADING-CUSTOM-ID]][Description::Heading text]]=.

Because only Org files can have links to individual headings, the
command ~denote-org-link-to-heading~ prompts only for Org files
(i.e. files which include the =.org= extension). Remember that Denote
works with many file types (read the Denote manual's section about the
file-naming scheme).

This feature is similar to the concept of the user option
~denote-org-store-link-to-heading~ (which is part of the main ~denote~
package). It is, however, interactive and differs in the
directionality of the action. With that user option, the command
~org-store-link~ will generate a =CUSTOM_ID= for the current heading
(or capture the value of one as-is), giving the user the option to
then call ~org-insert-link~ wherever they see fit. By contrast, the
command ~denote-org-link-to-heading~ prompts for a file, then a
heading, and inserts the link at point.

Just as with files, it is possible to show backlinks for the given
heading ([[#h:604bf92a-908a-485c-98b8-37ccae559afd][Backlinks for Org headings]]).

** Backlinks for Org headings
:PROPERTIES:
:CUSTOM_ID: h:604bf92a-908a-485c-98b8-37ccae559afd
:END:

The optional =denote-org.el= can generate Denote links to
individual headings ([[#h:fc1ad245-ec08-41be-8d1e-7153d99daf02][Insert link to an Org file with a further pointer to a heading]]).
It is then possible to produce a corresponding backlinks buffer with
the command ~denote-org-backlinks-for-heading~. The resulting
buffer behaves the same way as the standard backlinks buffer we
provide (read the Denote manual's section about the backlinks buffer).
An Org dynamic block with backlinks to the current heading is also an
option ([[#h:50160fae-6515-4d7d-9737-995ad925e64b][Org dynamic blocks to insert links or backlinks]]).

* Convert =denote:= links to =file:= links in Org and vice versa
:PROPERTIES:
:CUSTOM_ID: h:ed220cac-7dcb-4bb7-9243-1bb85e452e5f
:END:

Sometimes the user needs to translate all =denote:= link types to
their =file:= equivalent. This may be because some other tool does not
recognise =denote:= links (or other custom links types---which are a
standard feature of Org, by the way). The user thus needs to (i)
either make a copy of their Denote note or edit the existing one, and
(ii) convert all links to the generic =file:= link type that
external/other programs understand.

The optional extension =denote-org.el= contains two commands
that are relevant for this use-case:

#+findex: denote-org-convert-links-to-file-type
+ Convert =denote:= links to =file:= links :: The command
  ~denote-org-convert-links-to-file-type~ goes through the
  buffer to find all =denote:= links. It gets the identifier of the
  link and resolves it to the actual file system path. It then
  replaces the match so that the link is written with the =file:= type
  and then the file system path. The optional search terms and/or link
  description are preserved ([[#h:fc1ad245-ec08-41be-8d1e-7153d99daf02][Insert link to an Org file with a further pointer to a heading]]).

#+findex: denote-org-convert-links-to-denote-type
+ Convert =file:= links to =denote:= links :: The command
  ~denote-org-convert-links-to-denote-type~ behaves like the
  one above. The difference is that it finds the file system path and
  converts it into its identifier.

* Installation
:PROPERTIES:
:CUSTOM_ID: h:installation
:END:
#+cindex: Installation instructions

** GNU ELPA package
:PROPERTIES:
:CUSTOM_ID: h:gnu-elpa-package
:END:

The package is available as =denote-org=.  Simply do:

: M-x package-refresh-contents
: M-x package-install

And search for it.

GNU ELPA provides the latest stable release.  Those who prefer to follow
the development process in order to report bugs or suggest changes, can
use the version of the package from the GNU-devel ELPA archive.  Read:
https://protesilaos.com/codelog/2022-05-13-emacs-elpa-devel/.

** Manual installation
:PROPERTIES:
:CUSTOM_ID: h:manual-installation
:END:

Assuming your Emacs files are found in =~/.emacs.d/=, execute the
following commands in a shell prompt:

#+begin_src sh
cd ~/.emacs.d

# Create a directory for manually-installed packages
mkdir manual-packages

# Go to the new directory
cd manual-packages

# Clone this repo, naming it "denote-org"
git clone https://github.com/protesilaos/denote-org denote-org
#+end_src

Finally, in your =init.el= (or equivalent) evaluate this:

#+begin_src emacs-lisp
;; Make Elisp files in that directory available to the user.
(add-to-list 'load-path "~/.emacs.d/manual-packages/denote-org")
#+end_src

Everything is in place to set up the package.

* Sample configuration
:PROPERTIES:
:CUSTOM_ID: h:sample-configuration
:END:
#+cindex: Package configuration

#+begin_src emacs-lisp
(use-package denote-org
  :ensure t
  :commands
  ;; I list the commands here so that you can discover them more
  ;; easily.  You might want to bind the most frequently used ones to
  ;; the `org-mode-map'.
  ( denote-org-link-to-heading
    denote-org-backlinks-for-heading

    denote-org-extract-org-subtree

    denote-org-convert-links-to-file-type
    denote-org-convert-links-to-denote-type

    denote-org-dblock-insert-files
    denote-org-dblock-insert-links
    denote-org-dblock-insert-backlinks
    denote-org-dblock-insert-missing-links
    denote-org-dblock-insert-files-as-headings))
#+end_src

* Acknowledgements
:PROPERTIES:
:CUSTOM_ID: h:acknowledgements
:END:
#+cindex: Contributors

Denote Org is meant to be a collective effort.  Every bit of help matters.

+ Author/maintainer :: Protesilaos Stavrou.
+ Contributions to code or the manual :: Peter Prevos.
+ Ideas and user feedback :: GCamp6, Matt Nolan.

* GNU Free Documentation License
:PROPERTIES:
:APPENDIX: t
:CUSTOM_ID: h:gnu-free-documentation-license
:END:

#+texinfo: @include doclicense.texi

#+begin_export html
<pre>

                GNU Free Documentation License
                 Version 1.3, 3 November 2008


 Copyright (C) 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc.
     <https://fsf.org/>
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.

0. PREAMBLE

The purpose of this License is to make a manual, textbook, or other
functional and useful document "free" in the sense of freedom: to
assure everyone the effective freedom to copy and redistribute it,
with or without modifying it, either commercially or noncommercially.
Secondarily, this License preserves for the author and publisher a way
to get credit for their work, while not being considered responsible
for modifications made by others.

This License is a kind of "copyleft", which means that derivative
works of the document must themselves be free in the same sense.  It
complements the GNU General Public License, which is a copyleft
license designed for free software.

We have designed this License in order to use it for manuals for free
software, because free software needs free documentation: a free
program should come with manuals providing the same freedoms that the
software does.  But this License is not limited to software manuals;
it can be used for any textual work, regardless of subject matter or
whether it is published as a printed book.  We recommend this License
principally for works whose purpose is instruction or reference.


1. APPLICABILITY AND DEFINITIONS

This License applies to any manual or other work, in any medium, that
contains a notice placed by the copyright holder saying it can be
distributed under the terms of this License.  Such a notice grants a
world-wide, royalty-free license, unlimited in duration, to use that
work under the conditions stated herein.  The "Document", below,
refers to any such manual or work.  Any member of the public is a
licensee, and is addressed as "you".  You accept the license if you
copy, modify or distribute the work in a way requiring permission
under copyright law.

A "Modified Version" of the Document means any work containing the
Document or a portion of it, either copied verbatim, or with
modifications and/or translated into another language.

A "Secondary Section" is a named appendix or a front-matter section of
the Document that deals exclusively with the relationship of the
publishers or authors of the Document to the Document's overall
subject (or to related matters) and contains nothing that could fall
directly within that overall subject.  (Thus, if the Document is in
part a textbook of mathematics, a Secondary Section may not explain
any mathematics.)  The relationship could be a matter of historical
connection with the subject or with related matters, or of legal,
commercial, philosophical, ethical or political position regarding
them.

The "Invariant Sections" are certain Secondary Sections whose titles
are designated, as being those of Invariant Sections, in the notice
that says that the Document is released under this License.  If a
section does not fit the above definition of Secondary then it is not
allowed to be designated as Invariant.  The Document may contain zero
Invariant Sections.  If the Document does not identify any Invariant
Sections then there are none.

The "Cover Texts" are certain short passages of text that are listed,
as Front-Cover Texts or Back-Cover Texts, in the notice that says that
the Document is released under this License.  A Front-Cover Text may
be at most 5 words, and a Back-Cover Text may be at most 25 words.

A "Transparent" copy of the Document means a machine-readable copy,
represented in a format whose specification is available to the
general public, that is suitable for revising the document
straightforwardly with generic text editors or (for images composed of
pixels) generic paint programs or (for drawings) some widely available
drawing editor, and that is suitable for input to text formatters or
for automatic translation to a variety of formats suitable for input
to text formatters.  A copy made in an otherwise Transparent file
format whose markup, or absence of markup, has been arranged to thwart
or discourage subsequent modification by readers is not Transparent.
An image format is not Transparent if used for any substantial amount
of text.  A copy that is not "Transparent" is called "Opaque".

Examples of suitable formats for Transparent copies include plain
ASCII without markup, Texinfo input format, LaTeX input format, SGML
or XML using a publicly available DTD, and standard-conforming simple
HTML, PostScript or PDF designed for human modification.  Examples of
transparent image formats include PNG, XCF and JPG.  Opaque formats
include proprietary formats that can be read and edited only by
proprietary word processors, SGML or XML for which the DTD and/or
processing tools are not generally available, and the
machine-generated HTML, PostScript or PDF produced by some word
processors for output purposes only.

The "Title Page" means, for a printed book, the title page itself,
plus such following pages as are needed to hold, legibly, the material
this License requires to appear in the title page.  For works in
formats which do not have any title page as such, "Title Page" means
the text near the most prominent appearance of the work's title,
preceding the beginning of the body of the text.

The "publisher" means any person or entity that distributes copies of
the Document to the public.

A section "Entitled XYZ" means a named subunit of the Document whose
title either is precisely XYZ or contains XYZ in parentheses following
text that translates XYZ in another language.  (Here XYZ stands for a
specific section name mentioned below, such as "Acknowledgements",
"Dedications", "Endorsements", or "History".)  To "Preserve the Title"
of such a section when you modify the Document means that it remains a
section "Entitled XYZ" according to this definition.

The Document may include Warranty Disclaimers next to the notice which
states that this License applies to the Document.  These Warranty
Disclaimers are considered to be included by reference in this
License, but only as regards disclaiming warranties: any other
implication that these Warranty Disclaimers may have is void and has
no effect on the meaning of this License.

2. VERBATIM COPYING

You may copy and distribute the Document in any medium, either
commercially or noncommercially, provided that this License, the
copyright notices, and the license notice saying this License applies
to the Document are reproduced in all copies, and that you add no
other conditions whatsoever to those of this License.  You may not use
technical measures to obstruct or control the reading or further
copying of the copies you make or distribute.  However, you may accept
compensation in exchange for copies.  If you distribute a large enough
number of copies you must also follow the conditions in section 3.

You may also lend copies, under the same conditions stated above, and
you may publicly display copies.


3. COPYING IN QUANTITY

If you publish printed copies (or copies in media that commonly have
printed covers) of the Document, numbering more than 100, and the
Document's license notice requires Cover Texts, you must enclose the
copies in covers that carry, clearly and legibly, all these Cover
Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on
the back cover.  Both covers must also clearly and legibly identify
you as the publisher of these copies.  The front cover must present
the full title with all words of the title equally prominent and
visible.  You may add other material on the covers in addition.
Copying with changes limited to the covers, as long as they preserve
the title of the Document and satisfy these conditions, can be treated
as verbatim copying in other respects.

If the required texts for either cover are too voluminous to fit
legibly, you should put the first ones listed (as many as fit
reasonably) on the actual cover, and continue the rest onto adjacent
pages.

If you publish or distribute Opaque copies of the Document numbering
more than 100, you must either include a machine-readable Transparent
copy along with each Opaque copy, or state in or with each Opaque copy
a computer-network location from which the general network-using
public has access to download using public-standard network protocols
a complete Transparent copy of the Document, free of added material.
If you use the latter option, you must take reasonably prudent steps,
when you begin distribution of Opaque copies in quantity, to ensure
that this Transparent copy will remain thus accessible at the stated
location until at least one year after the last time you distribute an
Opaque copy (directly or through your agents or retailers) of that
edition to the public.

It is requested, but not required, that you contact the authors of the
Document well before redistributing any large number of copies, to
give them a chance to provide you with an updated version of the
Document.


4. MODIFICATIONS

You may copy and distribute a Modified Version of the Document under
the conditions of sections 2 and 3 above, provided that you release
the Modified Version under precisely this License, with the Modified
Version filling the role of the Document, thus licensing distribution
and modification of the Modified Version to whoever possesses a copy
of it.  In addition, you must do these things in the Modified Version:

A. Use in the Title Page (and on the covers, if any) a title distinct
   from that of the Document, and from those of previous versions
   (which should, if there were any, be listed in the History section
   of the Document).  You may use the same title as a previous version
   if the original publisher of that version gives permission.
B. List on the Title Page, as authors, one or more persons or entities
   responsible for authorship of the modifications in the Modified
   Version, together with at least five of the principal authors of the
   Document (all of its principal authors, if it has fewer than five),
   unless they release you from this requirement.
C. State on the Title page the name of the publisher of the
   Modified Version, as the publisher.
D. Preserve all the copyright notices of the Document.
E. Add an appropriate copyright notice for your modifications
   adjacent to the other copyright notices.
F. Include, immediately after the copyright notices, a license notice
   giving the public permission to use the Modified Version under the
   terms of this License, in the form shown in the Addendum below.
G. Preserve in that license notice the full lists of Invariant Sections
   and required Cover Texts given in the Document's license notice.
H. Include an unaltered copy of this License.
I. Preserve the section Entitled "History", Preserve its Title, and add
   to it an item stating at least the title, year, new authors, and
   publisher of the Modified Version as given on the Title Page.  If
   there is no section Entitled "History" in the Document, create one
   stating the title, year, authors, and publisher of the Document as
   given on its Title Page, then add an item describing the Modified
   Version as stated in the previous sentence.
J. Preserve the network location, if any, given in the Document for
   public access to a Transparent copy of the Document, and likewise
   the network locations given in the Document for previous versions
   it was based on.  These may be placed in the "History" section.
   You may omit a network location for a work that was published at
   least four years before the Document itself, or if the original
   publisher of the version it refers to gives permission.
K. For any section Entitled "Acknowledgements" or "Dedications",
   Preserve the Title of the section, and preserve in the section all
   the substance and tone of each of the contributor acknowledgements
   and/or dedications given therein.
L. Preserve all the Invariant Sections of the Document,
   unaltered in their text and in their titles.  Section numbers
   or the equivalent are not considered part of the section titles.
M. Delete any section Entitled "Endorsements".  Such a section
   may not be included in the Modified Version.
N. Do not retitle any existing section to be Entitled "Endorsements"
   or to conflict in title with any Invariant Section.
O. Preserve any Warranty Disclaimers.

If the Modified Version includes new front-matter sections or
appendices that qualify as Secondary Sections and contain no material
copied from the Document, you may at your option designate some or all
of these sections as invariant.  To do this, add their titles to the
list of Invariant Sections in the Modified Version's license notice.
These titles must be distinct from any other section titles.

You may add a section Entitled "Endorsements", provided it contains
nothing but endorsements of your Modified Version by various
parties--for example, statements of peer review or that the text has
been approved by an organization as the authoritative definition of a
standard.

You may add a passage of up to five words as a Front-Cover Text, and a
passage of up to 25 words as a Back-Cover Text, to the end of the list
of Cover Texts in the Modified Version.  Only one passage of
Front-Cover Text and one of Back-Cover Text may be added by (or
through arrangements made by) any one entity.  If the Document already
includes a cover text for the same cover, previously added by you or
by arrangement made by the same entity you are acting on behalf of,
you may not add another; but you may replace the old one, on explicit
permission from the previous publisher that added the old one.

The author(s) and publisher(s) of the Document do not by this License
give permission to use their names for publicity for or to assert or
imply endorsement of any Modified Version.


5. COMBINING DOCUMENTS

You may combine the Document with other documents released under this
License, under the terms defined in section 4 above for modified
versions, provided that you include in the combination all of the
Invariant Sections of all of the original documents, unmodified, and
list them all as Invariant Sections of your combined work in its
license notice, and that you preserve all their Warranty Disclaimers.

The combined work need only contain one copy of this License, and
multiple identical Invariant Sections may be replaced with a single
copy.  If there are multiple Invariant Sections with the same name but
different contents, make the title of each such section unique by
adding at the end of it, in parentheses, the name of the original
author or publisher of that section if known, or else a unique number.
Make the same adjustment to the section titles in the list of
Invariant Sections in the license notice of the combined work.

In the combination, you must combine any sections Entitled "History"
in the various original documents, forming one section Entitled
"History"; likewise combine any sections Entitled "Acknowledgements",
and any sections Entitled "Dedications".  You must delete all sections
Entitled "Endorsements".


6. COLLECTIONS OF DOCUMENTS

You may make a collection consisting of the Document and other
documents released under this License, and replace the individual
copies of this License in the various documents with a single copy
that is included in the collection, provided that you follow the rules
of this License for verbatim copying of each of the documents in all
other respects.

You may extract a single document from such a collection, and
distribute it individually under this License, provided you insert a
copy of this License into the extracted document, and follow this
License in all other respects regarding verbatim copying of that
document.


7. AGGREGATION WITH INDEPENDENT WORKS

A compilation of the Document or its derivatives with other separate
and independent documents or works, in or on a volume of a storage or
distribution medium, is called an "aggregate" if the copyright
resulting from the compilation is not used to limit the legal rights
of the compilation's users beyond what the individual works permit.
When the Document is included in an aggregate, this License does not
apply to the other works in the aggregate which are not themselves
derivative works of the Document.

If the Cover Text requirement of section 3 is applicable to these
copies of the Document, then if the Document is less than one half of
the entire aggregate, the Document's Cover Texts may be placed on
covers that bracket the Document within the aggregate, or the
electronic equivalent of covers if the Document is in electronic form.
Otherwise they must appear on printed covers that bracket the whole
aggregate.


8. TRANSLATION

Translation is considered a kind of modification, so you may
distribute translations of the Document under the terms of section 4.
Replacing Invariant Sections with translations requires special
permission from their copyright holders, but you may include
translations of some or all Invariant Sections in addition to the
original versions of these Invariant Sections.  You may include a
translation of this License, and all the license notices in the
Document, and any Warranty Disclaimers, provided that you also include
the original English version of this License and the original versions
of those notices and disclaimers.  In case of a disagreement between
the translation and the original version of this License or a notice
or disclaimer, the original version will prevail.

If a section in the Document is Entitled "Acknowledgements",
"Dedications", or "History", the requirement (section 4) to Preserve
its Title (section 1) will typically require changing the actual
title.


9. TERMINATION

You may not copy, modify, sublicense, or distribute the Document
except as expressly provided under this License.  Any attempt
otherwise to copy, modify, sublicense, or distribute it is void, and
will automatically terminate your rights under this License.

However, if you cease all violation of this License, then your license
from a particular copyright holder is reinstated (a) provisionally,
unless and until the copyright holder explicitly and finally
terminates your license, and (b) permanently, if the copyright holder
fails to notify you of the violation by some reasonable means prior to
60 days after the cessation.

Moreover, your license from a particular copyright holder is
reinstated permanently if the copyright holder notifies you of the
violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
copyright holder, and you cure the violation prior to 30 days after
your receipt of the notice.

Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License.  If your rights have been terminated and not permanently
reinstated, receipt of a copy of some or all of the same material does
not give you any rights to use it.


10. FUTURE REVISIONS OF THIS LICENSE

The Free Software Foundation may publish new, revised versions of the
GNU Free Documentation License from time to time.  Such new versions
will be similar in spirit to the present version, but may differ in
detail to address new problems or concerns.  See
https://www.gnu.org/licenses/.

Each version of the License is given a distinguishing version number.
If the Document specifies that a particular numbered version of this
License "or any later version" applies to it, you have the option of
following the terms and conditions either of that specified version or
of any later version that has been published (not as a draft) by the
Free Software Foundation.  If the Document does not specify a version
number of this License, you may choose any version ever published (not
as a draft) by the Free Software Foundation.  If the Document
specifies that a proxy can decide which future versions of this
License can be used, that proxy's public statement of acceptance of a
version permanently authorizes you to choose that version for the
Document.

11. RELICENSING

"Massive Multiauthor Collaboration Site" (or "MMC Site") means any
World Wide Web server that publishes copyrightable works and also
provides prominent facilities for anybody to edit those works.  A
public wiki that anybody can edit is an example of such a server.  A
"Massive Multiauthor Collaboration" (or "MMC") contained in the site
means any set of copyrightable works thus published on the MMC site.

"CC-BY-SA" means the Creative Commons Attribution-Share Alike 3.0
license published by Creative Commons Corporation, a not-for-profit
corporation with a principal place of business in San Francisco,
California, as well as future copyleft versions of that license
published by that same organization.

"Incorporate" means to publish or republish a Document, in whole or in
part, as part of another Document.

An MMC is "eligible for relicensing" if it is licensed under this
License, and if all works that were first published under this License
somewhere other than this MMC, and subsequently incorporated in whole or
in part into the MMC, (1) had no cover texts or invariant sections, and
(2) were thus incorporated prior to November 1, 2008.

The operator of an MMC Site may republish an MMC contained in the site
under CC-BY-SA on the same site at any time before August 1, 2009,
provided the MMC is eligible for relicensing.


ADDENDUM: How to use this License for your documents

To use this License in a document you have written, include a copy of
the License in the document and put the following copyright and
license notices just after the title page:

    Copyright (c)  YEAR  YOUR NAME.
    Permission is granted to copy, distribute and/or modify this document
    under the terms of the GNU Free Documentation License, Version 1.3
    or any later version published by the Free Software Foundation;
    with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
    A copy of the license is included in the section entitled "GNU
    Free Documentation License".

If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts,
replace the "with...Texts." line with this:

    with the Invariant Sections being LIST THEIR TITLES, with the
    Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.

If you have Invariant Sections without Cover Texts, or some other
combination of the three, merge those two alternatives to suit the
situation.

If your document contains nontrivial examples of program code, we
recommend releasing these examples in parallel under your choice of
free software license, such as the GNU General Public License,
to permit their use in free software.
</pre>
#+end_export

#+html: <!--

* Indices
:PROPERTIES:
:CUSTOM_ID: h:indices
:END:

** Function index
:PROPERTIES:
:INDEX: fn
:CUSTOM_ID: h:function-index
:END:

** Variable index
:PROPERTIES:
:INDEX: vr
:CUSTOM_ID: h:variable-index
:END:

** Concept index
:PROPERTIES:
:INDEX: cp
:CUSTOM_ID: h:concept-index
:END:

#+html: -->
