v2.2.2 (#2171 )

(feat)log: init (#2170 )
Create initial log module for working with Org logs
2025-08-01 12:17:21 -05:00 · 2022-04-24 17:05:27 -07:00 · 2022-04-24 16:57:13 -07:00 · 2022-04-23 16:36:09 -07:00 · 2022-04-16 20:34:49 -07:00 · 2022-04-16 20:32:57 -07:00
26 changed files with 1811 additions and 901 deletions
--- a/.dir-locals.el
+++ b/.dir-locals.el
@ -4,6 +4,9 @@
  (elisp-lint-ignored-validators . ("byte-compile" "package-lint"))
  (elisp-lint-indent-specs . ((describe . 1)
                              (it . 1)
+                              (thread-first . 0)
+                              (cl-flet . 1)
+                              (cl-flet* . 1)
                              (org-element-map . defun)
                              (org-roam-dolist-with-progress . 2)
                              (org-roam-with-temp-buffer . 1)
--- a/.github/FUNDING.yml
+++ b/.github/FUNDING.yml
@ -1,6 +1,6 @@
 # These are supported funding model platforms

-github: [jethrokuan, zaeph]
+github: [jethrokuan]
 patreon: # Replace with a single Patreon username
 open_collective: # Replace with a single Open Collective username
 ko_fi: # Replace with a single Ko-fi username
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@ -39,5 +39,3 @@ Example:
 ### Environment

 <!-- Please M-x org-roam-diagnostics and paste results here -->
-
- Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@ -46,7 +46,7 @@ jobs:
      - uses: actions/checkout@v2

      - name: Install Eldev
-        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh
+        run: curl -fsSL https://raw.github.com/org-roam/org-roam/master/github-eldev | sh

      - name: Install dependencies
        run: make prepare
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@ -1,8 +1,64 @@
 # Changelog
-
-## TBD
+## 2.2.2
+### Breaking
 ### Added
- [#1806](https://github.com/org-roam/org-roam/pull/1806) db: support caching and usage of Org 9.5's in-built citations
+- [#2138](https://github.com/org-roam/org-roam/pull/2138) export: add new module
+- [#2170](https://github.com/org-roam/org-roam/pull/2170) log: add new module for working with org logs
+- [#2158](https://github.com/org-roam/org-roam/pull/2158) db: support emacsql-sqlite-builtin and emacsql-sqlite-module
+- [#2160](https://github.com/org-roam/org-roam/pull/2160) core: support a list of `org-roam-file-exclude-regexp`
+
+### Removed
+### Fixed
+- [#2091](https://github.com/org-roam/org-roam/pull/2091) node: fix org-roam-promote-entire-buffer structural errors
+- [#2130](https://github.com/org-roam/org-roam/pull/2130) buffer: unlinked-references section now also searches within symlinked directories
+- [#2152](https://github.com/org-roam/org-roam/pull/2152) org-roam-preview-default-function: doesn't copy copy content of next heading node when current node's content is empty
+- [#2159](https://github.com/org-roam/org-roam/pull/2159) db: fix db syncs on narrowed buffers
+- [#2156](https://github.com/org-roam/org-roam/pull/2157) capture: templates with functions are handled correctly to avoid signaling `char-or-string-p`
+
+### Changed
+- [#2160](https://github.com/org-roam/org-roam/pull/2160) core: ignore files in `org-attach-id-dir` by default
+
+## 2.2.1
+### Breaking
+- [#2054](https://github.com/org-roam/org-roam/pull/2054) node: simplify default `org-roam-node-display-template`.
+  This was done so completions work fine by default on all completion systems. To restore the tabular vertical completion interface, set this in your configuration:
+
+  ```emacs-lisp
+  (setq org-roam-node-display-template
+        (concat "${title:*} "
+                (propertize "${tags:10}" 'face 'org-tag)))
+  ```
+
+### Added
+- [#2042](https://github.com/org-roam/org-roam/pull/2042) db: add `org-roam-db-extra-links-elements` and `org-roam-db-extra-links-exclude-keys` for fine-grained control over additional link parsing
+- [#2049](https://github.com/org-roam/org-roam/pull/2049) capture: allow ID to be used as part of `org-roam-capture-templates`
+- [#2050](https://github.com/org-roam/org-roam/pull/2050) core: add `FILTER-FN` to `org-roam-node-random`
+- [#2065](https://github.com/org-roam/org-roam/pull/2065) dailies: add `keys` argument to the remaining dailies functions `org-roam-dailies-goto-yesterday`/`-today`/`-tomorrow`/`-date` and `org-roam-dailies-capture-yesterday`/`-tomorrow`/`-date` to give the abilty to get into a capture buffer bypassing the selection screen in all dailies commands. Extension of #2055
+- [#2079](https://github.com/org-roam/org-roam/pull/2079) capture: ensure that `:ref` info captured in all cases.
+- [#2121](https://github.com/org-roam/org-roam/pull/2121) buffer: add unique option to `org-roam-backlinks-section`
+
+### Removed
+### Fixed
+- [#2086](https://github.com/org-roam/org-roam/pull/2086) capture: correctly update org-id-locations on capture
+- [#2082](https://github.com/org-roam/org-roam/pull/2082) buffer: don't destroy window if `org-roam-node-toggle` reuses window
+- [#2080](https://github.com/org-roam/org-roam/pull/2080) dailies: prevent multiple "dailies/" subdir expansions
+- [#2055](https://github.com/org-roam/org-roam/pull/2055) dailies: removed stray f require, which was causing require and compilation errors
+- [#2117](https://github.com/org-roam/org-roam/pull/2117) capture: preserve trailing whitespace content in capture templates
+
+### Changed
+- [#2060](https://github.com/org-roam/org-roam/pull/2060) node: added double acute accent normalization for Unicode characters in titles
+- [#2040](https://github.com/org-roam/org-roam/pull/2040) completions: fix completions display-width for Helm users
+- [#2025](https://github.com/org-roam/org-roam/pull/2025) chore: removed the dependencies on f.el and s.el
+- [#2109](https://github.com/org-roam/org-roam/pull/2109) capture: `org-roam-node-insert` places cursor after inserted link where appropriate
+- [#2123](https://github.com/org-roam/org-roam/pull/2123), [#2124](https://github.com/org-roam/org-roam/pull/2124) buffer: `org-roam-mode-section-functions` renamed to `org-roam-mode-sections`, supports passing args into the section-rendering function
+
+## 2.2.0
+### Added
+- [#1806](https://github.com/org-roam/org-roam/pull/1806), [#2017](https://github.com/org-roam/org-roam/pull/2017) db: support caching and usage of Org 9.5's in-built citations
+- [#1963](https://github.com/org-roam/org-roam/pull/1963) db: cache file title into files table
+- [#1977](https://github.com/org-roam/org-roam/pull/1977) db: support Org-ref v3 citations
+- [#1907](https://github.com/org-roam/org-roam/pull/1907), [#2009](https://github.com/org-roam/org-roam/pull/2009), [#2018](https://github.com/org-roam/org-roam/pull/2018) db: support sqlite3
+- [#2028](https://github.com/org-roam/org-roam/pull/2028) dailies: add `keys` argument to `org-roam-dailies-capture-today` and `org-roam-dailies--capture` functions to give the abilty to get into a capture buffer bypassing the selection screen

 ### Removed
 ### Changed
@ -10,12 +66,22 @@
 - [#1809](https://github.com/org-roam/org-roam/pull/1809) capture: the mandatory `:if-new` property of each capture template is now renamed to `:target`
 - [#1829](https://github.com/org-roam/org-roam/pull/1829) perf: file sql updates are now wrapped in a transaction
 - [#1877](https://github.com/org-roam/org-roam/pull/1877) dailies: stop asking for time, only date
+- [#1949](https://github.com/org-roam/org-roam/pull/1949) db: check for property drawers are now case-insensitive

 ### Fixed
 - [#1798](https://github.com/org-roam/org-roam/pull/1798) org-roam-node-at-point: do not skip invisible headings
 - [#1807](https://github.com/org-roam/org-roam/pull/1807) capture: always trigger `:if-new` template for existing nodes
 - [#1813](https://github.com/org-roam/org-roam/pull/1813) db: prevent empty ROAM_ALIASES from crashing db updates
 - [#1816](https://github.com/org-roam/org-roam/pull/1816) db: prevent invalid ROAM_REFS from crashing db updates
+- [#1893](https://github.com/org-roam/org-roam/pull/1893), [#1896](https://github.com/org-roam/org-roam/pull/1896), [#1901](https://github.com/org-roam/org-roam/pull/1901), [#1895](https://github.com/org-roam/org-roam/pull/1895), [#1904](https://github.com/org-roam/org-roam/pull/1904) completions: various mini-buffer related completion fixes
+- [#1931](https://github.com/org-roam/org-roam/pull/1931) utils: org-roam-set-keyword now skips over all drawers
+- [#1947](https://github.com/org-roam/org-roam/pull/1947) db: links in ROAM_REFS are no longer considered as links
+- [#1948](https://github.com/org-roam/org-roam/pull/1948) completions: fix same-line completions
+- [#1953](https://github.com/org-roam/org-roam/pull/1953) db: refresh CATEGORY before writing to db
+- [#1946](https://github.com/org-roam/org-roam/pull/1946), [#1946](https://github.com/org-roam/org-roam/pull/1946), [#1958](https://github.com/org-roam/org-roam/pull/1958) various performance improvements
+- [#1980](https://github.com/org-roam/org-roam/pull/1980) utils: fix org-roam-with-file changing the minor-mode
+- [#2016](https://github.com/org-roam/org-roam/pull/2016) db: fix node caching being affected by agenda variables
+- [#2033](https://github.com/org-roam/org-roam/pull/2023) db: respect local variables during db parsing

 ## 2.1.0
 ### Added
--- a/README.md
+++ b/README.md
@ -47,30 +47,6 @@ Stable](https://stable.melpa.org/) using `package.el`:
 ```
 M-x package-install RET org-roam RET
 ```
-
-Here's a very basic sample for configuration of `org-roam` using `use-package`:
-
-```emacs-lisp
-(use-package org-roam
-  :ensure t
-  :custom
-  (org-roam-directory (file-truename "/path/to/org-files/"))
-  :bind (("C-c n l" . org-roam-buffer-toggle)
-         ("C-c n f" . org-roam-node-find)
-         ("C-c n g" . org-roam-graph)
-         ("C-c n i" . org-roam-node-insert)
-         ("C-c n c" . org-roam-capture)
-         ;; Dailies
-         ("C-c n j" . org-roam-dailies-capture-today))
-  :config
-  (org-roam-db-autosync-mode)
-  ;; If using org-roam-protocol
-  (require 'org-roam-protocol))
-```
-
-Note that the `file-truename` function is only necessary when you use symbolic
-link to `org-roam-directory`. Org-roam won't automatically resolve symbolic link
-to the directory.
 </details>

 ### Using `straight.el`
@ -198,6 +174,33 @@ Org-roam also comes with `.texi` files to integrate with Emacs' built-in Info
 system. Read the manual to find more details for how to install them manually.
 </details>

+## Configuration
+
+Here's a very basic sample for configuration of `org-roam` using `use-package`:
+
+```emacs-lisp
+(use-package org-roam
+  :ensure t
+  :custom
+  (org-roam-directory (file-truename "/path/to/org-files/"))
+  :bind (("C-c n l" . org-roam-buffer-toggle)
+         ("C-c n f" . org-roam-node-find)
+         ("C-c n g" . org-roam-graph)
+         ("C-c n i" . org-roam-node-insert)
+         ("C-c n c" . org-roam-capture)
+         ;; Dailies
+         ("C-c n j" . org-roam-dailies-capture-today))
+  :config
+  ;; If you're using a vertical completion framework, you might want a more informative completion interface
+  (setq org-roam-node-display-template (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag)))
+  (org-roam-db-autosync-mode)
+  ;; If using org-roam-protocol
+  (require 'org-roam-protocol))
+```
+
+Note that the `file-truename` function is only necessary when you use symbolic
+link to `org-roam-directory`. Org-roam won't automatically resolve symbolic link
+to the directory.
 ## Getting Started

 [David Wilson](https://github.com/daviwil) of [System
@ -225,7 +228,7 @@ it has not already been addressed on [GitHub][issues] or on

 - [Jethro Kuan](https://braindump.jethro.dev/)
  ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
- [Alexey Shmalko](https://braindump.rasen.dev/)
+- [Alexey Shmalko](https://www.alexeyshmalko.com/)
 - [Sidharth Arya](https://sidhartharya.github.io/braindump/index.html)

 ## Contributing
--- a/doc/org-roam.org
+++ b/doc/org-roam.org
@ -1,23 +1,23 @@
 #+title: Org-roam User Manual
 #+author: Jethro Kuan
 #+email: jethrokuan95@gmail.com
-#+date: 2020-2021
+#+date: 2020-2022
 #+language: en

 #+texinfo_deffn: t
 #+texinfo_dir_category: Emacs
 #+texinfo_dir_title: Org-roam: (org-roam).
 #+texinfo_dir_desc: Roam Research for Emacs.
-#+subtitle: for version 2.1.0
+#+subtitle: for version 2.2.1

 #+options: H:4 num:3 toc:nil creator:t ':t
 #+property: header-args :eval never
 #+texinfo: @noindent

-This manual is for Org-roam version 2.1.0.
+This manual is for Org-roam version 2.2.1.

 #+BEGIN_QUOTE
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+Copyright (C) 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 You can redistribute this document and/or modify it under the terms of the GNU
 General Public License as published by the Free Software Foundation, either
@ -134,7 +134,7 @@ A slip-box requires a method for quickly capturing ideas. These are called
 *fleeting notes*: they are simple reminders of information or ideas that will
 need to be processed later on, or trashed. This is typically accomplished using
 ~org-capture~ (see info:org#Capture), or using Org-roam's daily notes
-functionality (see [[*Org-roam Dailies][Org-roam Dailies]]). This provides a central inbox for collecting
+functionality (see [[*org-roam-dailies][org-roam-dailies]]). This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.

 *Permanent notes*
@ -288,29 +288,25 @@ in your Emacs environment as a prerequisite for Org-roam when you install it.
 ~emacsql-sqlite~ requires a C compiler (e.g. ~gcc~ or ~clang~) to be present in
 your computer. How to install a C compiler depends on the OS that you use.

- For Windows:
+**** C Compiler for Windows

-There are various ways to install one, depending on how you have installed
-Emacs. If you use Emacs within a Cygwin or MinGW environment, then you should
-install a compiler using their respective package manager.
+One of the easiest ways to install a C compiler in Windows is to use [[https://www.msys2.org/][MSYS2]] as at the time of this writing:

-If you have installed your Emacs from the [[https://www.gnu.org/software/emacs/][GNU Emacs website]], then the easiest way
-is to use [[https://www.msys2.org/][MSYS2]] as at the time of this writing:
-
-1. Use the installer in the official website and install MSYS2
-2. Run MSYS2
-3. In the command-line tool, type the following and answer "Y" to proceed:
+1. Download and use the installer in the official MSYS2 website
+2. Run MSYS2 and in its terminal, type the following and answer "Y" to
+   proceed -- this will install ~gcc~ in your PC:

   #+BEGIN_SRC bash
     pacman -S gcc
   #+END_SRC

-   Note that you do not need to manually set the PATH for MSYS2; the
-installer automatically takes care of it for you.
+4. On Windows, add ~C:\msys64\usr\bin~ (command =where gcc= in MSYS2 terminal
+   can tell you the correct path) to ~PATH~ in your environmental variables

-4. Open Emacs and call ~M-x org-roam-db-autosync-mode~
+5. Launch Emacs and call ~M-x org-roam-db-autosync-mode~ (launch Emacs after
+   defining the path, so that Emacs can recognize it)

-   This will automatically start compiling ~emacsql-sqlite~; you should see a
+This will automatically start compiling ~emacsql-sqlite~; you should see a
 message in minibuffer. It may take a while until compilation completes. Once
 complete, you should see a new file ~emacsql-sqlite.exe~ created in a subfolder
 named ~sqlite~ under ~emacsql-sqlite~ installation folder. It's typically in
@ -373,7 +369,12 @@ For this tutorial, create an empty directory, and set ~org-roam-directory~:
 #+END_SRC

 The ~file-truename~ function is only necessary when you use symbolic links
-inside ~org-roam-directory~: Org-roam does not resolve symbolic links.
+inside ~org-roam-directory~: Org-roam does not resolve symbolic links. One can
+however instruct Emacs to always resolve symlinks, at a performance cost:
+
+#+begin_src emacs-lisp
+  (setq find-file-visit-truename t)
+#+end_src

 Next, we setup Org-roam to run functions on file changes to maintain cache
 consistency. This is achieved by running ~M-x org-roam-db-autosync-mode~. To
@ -417,6 +418,54 @@ brought through the node creation process.
 One can also conveniently insert links via the completion-at-point functions
 Org-roam provides (see [[*Completion][Completion]]).

+** Customizing Node Completions
+
+Node selection is achieved via the ~completing-read~ interface, typically
+through `org-roam-node-read`. The presentation of these nodes are governed by
+~org-roam-node-display-template~.
+
+- Variable: org-roam-node-display-template
+
+  Configures display formatting for Org-roam node.
+
+  Patterns of form "${field-name:length}" are interpolated based
+  on the current node.
+
+  Each "field-name" is replaced with the return value of each
+  corresponding accessor function for org-roam-node, e.g.
+  "${title}" will be interpolated by the result of
+  org-roam-node-title. You can also define custom accessors using
+  cl-defmethod. For example, you can define:
+
+    (cl-defmethod org-roam-node-my-title ((node org-roam-node))
+      (concat "My " (org-roam-node-title node)))
+
+  and then reference it here or in the capture templates as
+  "${my-title}".
+
+  "length" is an optional specifier and declares how many
+  characters can be used to display the value of the corresponding
+  field. If it's not specified, the field will be inserted as is,
+  i.e. it won't be aligned nor trimmed. If it's an integer, the
+  field will be aligned accordingly and all the exceeding
+  characters will be trimmed out. If it's "*", the field will use
+  as many characters as possible and will be aligned accordingly.
+
+  A closure can also be assigned to this variable in which case the
+  closure is evaluated and the return value is used as the
+  template. The closure must evaluate to a valid template string.
+
+If you're using a vertical completion framework, such as Ivy and Selectrum,
+Org-roam supports the generation of an aligned, tabular completion interface.
+For example, to include a column for tags up to 10 character widths wide, one
+can set ~org-roam-node-display-template~ as such:
+
+#+begin_src emacs-lisp
+  (setq org-roam-node-display-template
+        (concat "${title:*} "
+                (propertize "${tags:10}" 'face 'org-tag)))
+#+end_src
+
 * Customizing Node Caching
 ** How to cache

@ -489,6 +538,35 @@ all headlines with the ~ATTACH~ tag from the Org-roam database, one can set:
        (not (member "ATTACH" (org-get-tags)))))
 #+end_src

+Org-roam relied on the obtained Org AST for the buffer to parse links. However,
+links appearing in some places (e.g. within property drawers) are not considered
+by the Org AST to be links. Therefore, Org-roam takes special care of
+additionally trying to process these links. Use
+~org-roam-db-extra-links-elements~ to specify which additional Org AST element
+types to consider.
+
+- Variable: org-roam-db-extra-links-elements
+
+  The list of Org element types to include for parsing by Org-roam.
+
+  By default, when parsing Org's AST, links within keywords and
+  property drawers are not parsed as links. Sometimes however, it
+  is desirable to parse and cache these links (e.g. hiding links in
+  a property drawer).
+
+Additionally, one may want to ignore certain keys from being excluded within
+property drawers. For example, we would not want ~ROAM_REFS~ links to be
+self-referential. Hence, to exclude specific keys, we use
+~org-roam-db-extra-links-exclude-keys~.
+
+- Variable: org-roam-db-extra-links-exclude-keys
+
+  Keys to ignore when mapping over links.
+
+  The car of the association list is the Org element type (e.g. keyword). The
+  cdr is a list of case-insensitive strings to exclude from being treated as
+  links.
+
 ** When to cache

 By default, Org-roam is eager in caching: each time an Org-roam file is modified
@ -555,10 +633,10 @@ There are currently 3 provided widget types:
 - Unlinked references :: View nodes that contain text that match the nodes
  title/alias but are not linked

-To configure what sections are displayed in the buffer, set ~org-roam-mode-section-functions~.
+To configure what sections are displayed in the buffer, set ~org-roam-mode-sections.

 #+begin_src emacs-lisp
-  (setq org-roam-mode-section-functions
+  (setq org-roam-mode-sections
        (list #'org-roam-backlinks-section
              #'org-roam-reflinks-section
              ;; #'org-roam-unlinked-references-section
@ -567,6 +645,16 @@ To configure what sections are displayed in the buffer, set ~org-roam-mode-secti

 Note that computing unlinked references may be slow, and has not been added in by default.

+For each section function, you can pass args along to modify its behaviour. For
+example, if you want to render unique sources for backlinks (and also keep
+rendering reference links), set ~org-roam-mode-sections~ as follows:
+
+#+begin_src emacs-lisp
+  (setq org-roam-mode-sections
+        '((org-roam-backlinks-section :unique t)
+          org-roam-reflinks-section))
+#+end_src
+
 ** Configuring the Org-roam buffer display

 Org-roam does not control how the pop-up buffer is displayed: this is left to
@ -674,7 +762,7 @@ With the above example, if another node links to https://www.google.com/, it
 will show up as a “reference backlink”.

 These keys also come in useful for when taking website notes, using the
- ~roam-ref~ protocol (see [[*Org-roam Protocol][Roam Protocol]]).
+ ~roam-ref~ protocol (see [[*org-roam-protocol][org-roam-protocol]]).

 You may assign multiple refs to a single node, for example when you want
 multiple papers in a series to share the same note, or an article has a citation
@ -715,6 +803,16 @@ citation key:
 :END:
 #+end_src

+or
+
+#+begin_src org
+,* Probabilistic Robotics
+:PROPERTIES:
+:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
+:ROAM_REFS: [cite:@thrun2005probabilistic]
+:END:
+#+end_src
+
 for ~org-cite~, or:

 #+begin_src org
@ -795,202 +893,6 @@ Note that the Org-roam database stores metadata information in plain-text
 (headline text, for example), so if this information is private to you then you
 should also ensure the database is encrypted.

-* Org-roam Protocol
-
-Org-roam provides extensions for capturing content from external applications
-such as the browser, via ~org-protocol~. Org-roam extends ~org-protocol~ with 2
-protocols: the ~roam-node~ and ~roam-ref~ protocols.
-
-** Installation
-
-To enable Org-roam's protocol extensions, simply add the following to your init
-file:
-
-#+BEGIN_SRC emacs-lisp
-(require 'org-roam-protocol)
-#+END_SRC
-
-We also need to set up ~org-protocol~: the instructions for setting up
-~org-protocol~ are reproduced below.
-
-*** Linux
-For Linux users, create a desktop application in
-~~/.local/share/applications/org-protocol.desktop~:
-
-#+begin_example
-[Desktop Entry]
-Name=Org-Protocol
-Exec=emacsclient %u
-Icon=emacs-icon
-Type=Application
-Terminal=false
-MimeType=x-scheme-handler/org-protocol
-#+end_example
-
-Associate ~org-protocol://~ links with the desktop application by
-running in your shell:
-
-#+BEGIN_SRC bash
-xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
-#+END_SRC
-
-To disable the "confirm" prompt in Chrome, you can also make Chrome show a
-checkbox to tick, so that the ~Org-Protocol Client~ app will be used without
-confirmation. To do this, run in a shell:
-
-#+BEGIN_SRC bash
-sudo mkdir -p /etc/opt/chrome/policies/managed/
-sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
-{
-  "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
-}
-EOF
-sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
-#+END_SRC
-
-and then restart Chrome (for example, by navigating to <chrome://restart>) to
-make the new policy take effect.
-
-See [[https://www.chromium.org/administrators/linux-quick-start][here]] for more info on the ~/etc/opt/chrome/policies/managed~ directory and
-[[https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox][here]] for information on the ~ExternalProtocolDialogShowAlwaysOpenCheckbox~ policy.
-
-*** Mac OS
-For Mac OS, we need to create our own application.
-
-1. Launch Script Editor
-2. Use the following script, paying attention to the path to ~emacsclient~:
-
-#+begin_src emacs-lisp
-  on open location this_URL
-      set EC to "/usr/local/bin/emacsclient --no-wait "
-      set filePath to quoted form of this_URL
-      do shell script EC & filePath
-      tell application "Emacs" to activate
-  end open location
-#+end_src
-
-3. Save the script in ~/Applications/OrgProtocolClient.app~, changing the script type to
-   "Application", rather than "Script".
-4. Edit ~/Applications/OrgProtocolClient.app/Contents/Info.plist~, adding the
-   following before the last ~</dict>~ tag:
-
-#+begin_src text
-  <key>CFBundleURLTypes</key>
-  <array>
-    <dict>
-      <key>CFBundleURLName</key>
-      <string>org-protocol handler</string>
-      <key>CFBundleURLSchemes</key>
-      <array>
-        <string>org-protocol</string>
-      </array>
-    </dict>
-  </array>
-#+end_src
-
-5. Save the file, and run the ~OrgProtocolClient.app~ to register the protocol.
-
-To disable the "confirm" prompt in Chrome, you can also make Chrome
-show a checkbox to tick, so that the ~OrgProtocol~ app will be used
-without confirmation. To do this, run in a shell:
-
-#+BEGIN_SRC bash
-defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
-#+END_SRC
-
-If you're using [[https://github.com/railwaycat/homebrew-emacsmacport][Emacs Mac Port]], it registered its `Emacs.app` as the default
-handler for the URL scheme `org-protocol`. To make ~OrgProtocol.app~
-the default handler instead, run:
-
-#+BEGIN_SRC bash
-defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
-'{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
-#+END_SRC
-
-Then restart your computer.
-
-**** Testing org-protocol
-
-To test that you have the handler setup and registered properly from the command
-line you can run:
-
-#+begin_src bash
-  open org-protocol://roam-ref\?template=r\&ref=test\&title=this
-#+end_src
-
-If you get an error similar too this or the wrong handler is run:
-
-#+begin_quote
-No application knows how to open URL org-protocol://roam-ref?template=r&ref=test&title=this (Error Domain=NSOSStatusErrorDomain Code=-10814 "kLSApplicationNotFoundErr: E.g. no application claims the file" UserInfo={_LSLine=1489, _LSFunction=runEvaluator}).
-
-#+end_quote
-
-You may need to manually register your handler, like this:
-
-#+begin_src bash
-/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
-#+end_src
-
-Here is a link to the lsregister command that is really useful: https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/
-*** Windows
-For Windows, create a temporary ~org-protocol.reg~ file:
-
-#+BEGIN_SRC text
-REGEDIT4
-
-[HKEY_CLASSES_ROOT\org-protocol]
-@="URL:Org Protocol"
-"URL Protocol"=""
-[HKEY_CLASSES_ROOT\org-protocol\shell]
-[HKEY_CLASSES_ROOT\org-protocol\shell\open]
-[HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
-@="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""
-#+END_SRC
-
-The above will forward the protocol to WSL. If you run Emacs natively on
-Windows, replace the last line with:
-
-#+BEGIN_SRC text
-@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
-#+END_SRC
-
-After executing the .reg file, the protocol is registered and you can delete the
-file.
-
-** The roam-node protocol
-
-The roam-node protocol opens the node with ID specified by the ~node~ key (e.g.
-~org-protocol://roam-node?node=node-id~). ~org-roam-graph~ uses this to make the
-graph navigable.
-
-** The roam-ref protocol
-
-This protocol finds or creates a new note with a given ~ROAM_REFS~:
-
-[[file:images/roam-ref.gif]]
-
-To use this, create the following [[https://en.wikipedia.org/wiki/Bookmarklet][bookmarklet]] in your browser:
-
-#+BEGIN_SRC javascript
-  javascript:location.href =
-      'org-protocol://roam-ref?template=r&ref='
-      + encodeURIComponent(location.href)
-      + '&title='
-      + encodeURIComponent(document.title)
-      + '&body='
-      + encodeURIComponent(window.getSelection())
-#+END_SRC
-
-or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
-[[https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc][Configuring qutebrowser]]):
-
-#+BEGIN_SRC python
-  config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)")
-#+END_SRC
-
-where ~template~ is the template key for a template in
-~org-roam-capture-ref-templates~ (see [[*The Templating System][The Templating System]]).
-
 * The Templating System

 Org-roam extends the ~org-capture~ system, providing a smoother note-taking
@ -1072,12 +974,217 @@ One can check the list of available keys for nodes by inspecting the

 This makes ~${file}~, ~${file-hash}~ etc. all valid substitutions.

-* Graphing
+* Extensions
+** org-roam-protocol
+
+Org-roam provides extensions for capturing content from external applications
+such as the browser, via ~org-protocol~. Org-roam extends ~org-protocol~ with 2
+protocols: the ~roam-node~ and ~roam-ref~ protocols.
+
+*** Installation
+
+To enable Org-roam's protocol extensions, simply add the following to your init
+file:
+
+#+BEGIN_SRC emacs-lisp
+(require 'org-roam-protocol)
+#+END_SRC
+
+We also need to set up ~org-protocol~: the instructions for setting up
+~org-protocol~ are reproduced here.
+
+On a high-level, external calls are passed to Emacs via ~emacsclient~.
+~org-protocol~ intercepts these and runs custom actions based on the protocols
+registered. Hence, to use ~org-protocol~, once must:
+
+1. launch the ~emacsclient~ process
+2. Register ~org-protocol://~ as a valid scheme-handler
+
+The instructions for the latter for each operating system is detailed below.
+
+**** Linux
+For Linux users, create a desktop application in
+~~/.local/share/applications/org-protocol.desktop~:
+
+#+begin_example
+[Desktop Entry]
+Name=Org-Protocol
+Exec=emacsclient %u
+Icon=emacs-icon
+Type=Application
+Terminal=false
+MimeType=x-scheme-handler/org-protocol
+#+end_example
+
+Associate ~org-protocol://~ links with the desktop application by
+running in your shell:
+
+#+BEGIN_SRC bash
+xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
+#+END_SRC
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome show a
+checkbox to tick, so that the ~Org-Protocol Client~ app will be used without
+confirmation. To do this, run in a shell:
+
+#+BEGIN_SRC bash
+sudo mkdir -p /etc/opt/chrome/policies/managed/
+sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
+{
+  "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
+}
+EOF
+sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
+#+END_SRC
+
+and then restart Chrome (for example, by navigating to <chrome://restart>) to
+make the new policy take effect.
+
+See [[https://www.chromium.org/administrators/linux-quick-start][here]] for more info on the ~/etc/opt/chrome/policies/managed~ directory and
+[[https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox][here]] for information on the ~ExternalProtocolDialogShowAlwaysOpenCheckbox~ policy.
+
+**** Mac OS
+For Mac OS, we need to create our own application.
+
+1. Launch Script Editor
+2. Use the following script, paying attention to the path to ~emacsclient~:
+
+#+begin_src emacs-lisp
+  on open location this_URL
+      set EC to "/usr/local/bin/emacsclient --no-wait "
+      set filePath to quoted form of this_URL
+      do shell script EC & filePath
+      tell application "Emacs" to activate
+  end open location
+#+end_src
+
+3. Save the script in ~/Applications/OrgProtocolClient.app~, changing the script type to
+   "Application", rather than "Script".
+4. Edit ~/Applications/OrgProtocolClient.app/Contents/Info.plist~, adding the
+   following before the last ~</dict>~ tag:
+
+#+begin_src text
+  <key>CFBundleURLTypes</key>
+  <array>
+    <dict>
+      <key>CFBundleURLName</key>
+      <string>org-protocol handler</string>
+      <key>CFBundleURLSchemes</key>
+      <array>
+        <string>org-protocol</string>
+      </array>
+    </dict>
+  </array>
+#+end_src
+
+5. Save the file, and run the ~OrgProtocolClient.app~ to register the protocol.
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the ~OrgProtocol~ app will be used
+without confirmation. To do this, run in a shell:
+
+#+BEGIN_SRC bash
+defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
+#+END_SRC
+
+If you're using [[https://github.com/railwaycat/homebrew-emacsmacport][Emacs Mac Port]], it registered its `Emacs.app` as the default
+handler for the URL scheme `org-protocol`. To make ~OrgProtocol.app~
+the default handler instead, run:
+
+#+BEGIN_SRC bash
+defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
+'{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
+#+END_SRC
+
+Then restart your computer.
+
+***** Testing org-protocol
+
+To test that you have the handler setup and registered properly from the command
+line you can run:
+
+#+begin_src bash
+  open org-protocol://roam-ref\?template=r\&ref=test\&title=this
+#+end_src
+
+If you get an error similar too this or the wrong handler is run:
+
+#+begin_quote
+No application knows how to open URL org-protocol://roam-ref?template=r&ref=test&title=this (Error Domain=NSOSStatusErrorDomain Code=-10814 "kLSApplicationNotFoundErr: E.g. no application claims the file" UserInfo={_LSLine=1489, _LSFunction=runEvaluator}).
+
+#+end_quote
+
+You may need to manually register your handler, like this:
+
+#+begin_src bash
+/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
+#+end_src
+
+Here is a link to the lsregister command that is really useful: https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/
+**** Windows
+For Windows, create a temporary ~org-protocol.reg~ file:
+
+#+BEGIN_SRC text
+REGEDIT4
+
+[HKEY_CLASSES_ROOT\org-protocol]
+@="URL:Org Protocol"
+"URL Protocol"=""
+[HKEY_CLASSES_ROOT\org-protocol\shell]
+[HKEY_CLASSES_ROOT\org-protocol\shell\open]
+[HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
+@="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""
+#+END_SRC
+
+The above will forward the protocol to WSL. If you run Emacs natively on
+Windows, replace the last line with:
+
+#+BEGIN_SRC text
+@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
+#+END_SRC
+
+After executing the .reg file, the protocol is registered and you can delete the
+file.
+
+*** The roam-node protocol
+
+The roam-node protocol opens the node with ID specified by the ~node~ key (e.g.
+~org-protocol://roam-node?node=node-id~). ~org-roam-graph~ uses this to make the
+graph navigable.
+
+*** The roam-ref protocol
+
+This protocol finds or creates a new note with a given ~ROAM_REFS~:
+
+[[file:images/roam-ref.gif]]
+
+To use this, create the following [[https://en.wikipedia.org/wiki/Bookmarklet][bookmarklet]] in your browser:
+
+#+BEGIN_SRC javascript
+  javascript:location.href =
+      'org-protocol://roam-ref?template=r&ref='
+      + encodeURIComponent(location.href)
+      + '&title='
+      + encodeURIComponent(document.title)
+      + '&body='
+      + encodeURIComponent(window.getSelection())
+#+END_SRC
+
+or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
+[[https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc][Configuring qutebrowser]]):
+
+#+BEGIN_SRC python
+  config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)")
+#+END_SRC
+
+where ~template~ is the template key for a template in
+~org-roam-capture-ref-templates~ (see [[*The Templating System][The Templating System]]).
+
+** org-roam-graph

 Org-roam provides basic graphing capabilities to explore interconnections
 between notes, in ~org-roam-graph~. This is done by performing SQL queries and
-generating images using [[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*Org-roam Protocol][Roam
-Protocol]].
+generating images using [[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*org-roam-protocol][org-roam-protocol]].

 The entry point to graph creation is ~org-roam-graph~.

@ -1118,7 +1225,7 @@ ARG may be any of the following values:
          (org-roam-graph--open (concat "file://///wsl$/Ubuntu" file)))))
  #+END_SRC

-** Graph Options
+*** Graph Options

 Graphviz provides many options for customizing the graph output, and Org-roam
 supports some of them. See https://graphviz.gitlab.io/_pages/doc/info/attrs.html
@ -1144,12 +1251,12 @@ for customizable options.
  Extra options for edges in the graphviz output (The "E" attributes).
  Example: ~'(("dir" . "back"))~

-* Org-roam Dailies
+** org-roam-dailies

 Org-roam provides journaling capabilities akin to
 Org-journal with ~org-roam-dailies~.

-** Configuration
+*** Configuration

 For ~org-roam-dailies~ to work, you need to define two variables:

@ -1175,7 +1282,7 @@ Here is a sane default configuration:

 See [[*The Templating System][The Templating System]] for creating new templates.

-** Usage
+*** Usage

 ~org-roam-dailies~ provides these interactive functions:

@ -1229,6 +1336,18 @@ There are also commands which allow you to use Emacs’s ~calendar~ to find the
 - Function: ~org-roam-dailies-goto-next-note~

  When in an daily-note, find the next one.
+** org-roam-export
+
+Because Org-roam files are plain org files, they can be exported easily using
+~org-export~ to a variety of formats, including ~html~ and ~pdf~. However,
+Org-roam relies heavily on ID links, which Org's html export has poor support
+of. To fix this, Org-roam provides a bunch of overrides to better support
+export. To use them, simply run:
+
+#+begin_src emacs-lisp
+  (require 'org-roam-export)
+#+end_src
+
 * Performance Optimization
 ** Garbage Collection

@ -1302,7 +1421,7 @@ The Deft interface can slow down quickly when the number of files get huge.

 [[https://github.com/bastibe/org-journal][Org-journal]] provides journaling capabilities to Org-mode. A lot of its
 functionalities have been incorporated into Org-roam under the name
-[[*Org-roam Dailies][~org-roam-dailies~]]. It remains a good tool if you want to isolate your verbose
+[[*org-roam-dailies][~org-roam-dailies~]]. It remains a good tool if you want to isolate your verbose
 journal entries from the ideas you would write on a scratchpad.

 #+BEGIN_SRC emacs-lisp
@ -1355,6 +1474,9 @@ documents (PDF, EPUB etc.) within Org-mode.

 ** Bibliography

+Org 9.5 added native citation and bibliography functionality, called "org-cite",
+which org-roam supports.
+
 [[https://github.com/org-roam/org-roam-bibtex][org-roam-bibtex]] offers tight integration between [[https://github.com/jkitchin/org-ref][org-ref]], [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] and
 ~org-roam~. This helps you manage your bibliographic notes under ~org-roam~.

@ -1527,6 +1649,20 @@ to the publishing directory.  Example code follows:
                                         (kill-buffer (file-name-nondirectory svg))
                                         (setq my-publish-time 0)))))
 #+end_src
+** I'm seeing this "Selecting deleted buffer" error. What do I do?
+
+The "selecting deleted buffer" error usually occurs when you don't have a
+working ~emacsql-sqlite~ executable. Org-roam relies on this executable to
+function properly, and doesn't catch this error. This issue is most commonly
+seen on Windows setups. You can browse through the various GitHub issues posted
+about this [[https://github.com/org-roam/org-roam/issues?q=is%3Aissue+selecting+deleted][here]].
+
+To fix this, you can try the following:
+
+1. If on Windows, try replacing your system binary with [[https://github.com/nobiot/emacsql-sqlite.exe][this one]] that has been proven
+   to work
+2. Use the ~emacsql-sqlite3~ option rather than compiling your own emacsql
+   binary (see [[*How to cache][How to cache]]).

 * Developer's Guide to Org-roam
 ** Org-roam's Design Principle
@ -1673,7 +1809,7 @@ When GOTO is non-nil, go the note without creating an entry."
 :END:

 #+BEGIN_QUOTE
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+Copyright (C) 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 You can redistribute this document and/or modify it under the terms
 of the GNU General Public License as published by the Free Software
--- a/doc/org-roam.texi
+++ b/doc/org-roam.texi
@ -8,7 +8,7 @@

@copying
@quotation
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@@gmail.com>
+Copyright (C) 2020-2022 Jethro Kuan <jethrokuan95@@gmail.com>

 You can redistribute this document and/or modify it under the terms
 of the GNU General Public License as published by the Free Software
@ -31,7 +31,7 @@ General Public License for more details.
@finalout
@titlepage
@title Org-roam User Manual
-@subtitle for version 2.1.0
+@subtitle for version 2.2.1
@author Jethro Kuan
@page
@vskip 0pt plus 1filll
@ -44,10 +44,10 @@ General Public License for more details.

@noindent

-This manual is for Org-roam version 2.1.0.
+This manual is for Org-roam version 2.2.1.

@quotation
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@@gmail.com>
+Copyright (C) 2020-2022 Jethro Kuan <jethrokuan95@@gmail.com>

 You can redistribute this document and/or modify it under the terms of the GNU
 General Public License as published by the Free Software Foundation, either
@ -73,10 +73,8 @@ General Public License for more details.
 * Citations::
 * Completion::
 * Encryption::
-* Org-roam Protocol::
 * The Templating System::
-* Graphing::
-* Org-roam Dailies::
+* Extensions::
 * Performance Optimization::
 * The Org-mode Ecosystem::
 * FAQ::
@ -100,12 +98,17 @@ Installation Troubleshooting

 * C Compiler::

+C Compiler
+
+* C Compiler for Windows::
+
 Getting Started

 * The Org-roam Node::
 * Links between Nodes::
 * Setting up Org-roam::
 * Creating and Linking Nodes::
+* Customizing Node Completions::

 Customizing Node Caching

@ -136,7 +139,19 @@ Completion
 * Completing within Link Brackets::
 * Completing anywhere::

-Org-roam Protocol
+The Templating System
+
+* Template Walkthrough::
+* Org-roam Template Expansion::
+
+Extensions
+
+* org-roam-protocol::
+* org-roam-graph::
+* org-roam-dailies::
+* org-roam-export::
+
+org-roam-protocol

 * Installation: Installation (1). 
 * The roam-node protocol::
@ -148,20 +163,11 @@ Installation
 * Mac OS::
 * Windows::

-Mac OS
-
-* Testing org-protocol::
-
-The Templating System
-
-* Template Walkthrough::
-* Org-roam Template Expansion::
-
-Graphing
+org-roam-graph

 * Graph Options::

-Org-roam Dailies
+org-roam-dailies

 * Configuration::
 * Usage::
@ -190,6 +196,7 @@ FAQ
 * How do I migrate from Roam Research?::
 * How to migrate from Org-roam v1?::
 * How do I publish my notes with an Internet-friendly graph?::
+* I'm seeing this ``Selecting deleted buffer'' error. What do I do?: I'm seeing this ``Selecting deleted buffer'' error What do I do?. 

 How do I publish my notes with an Internet-friendly graph?

@ -336,7 +343,7 @@ A slip-box requires a method for quickly capturing ideas. These are called
@strong{fleeting notes}: they are simple reminders of information or ideas that will
 need to be processed later on, or trashed. This is typically accomplished using
@code{org-capture} (see @ref{Capture,,,org,}), or using Org-roam's daily notes
-functionality (see @ref{Org-roam Dailies}). This provides a central inbox for collecting
+functionality (see @ref{org-roam-dailies}). This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.

@strong{Permanent notes}
@ -535,42 +542,39 @@ in your Emacs environment as a prerequisite for Org-roam when you install it.
@code{emacsql-sqlite} requires a C compiler (e.g. @code{gcc} or @code{clang}) to be present in
 your computer. How to install a C compiler depends on the OS that you use.

-@itemize
-@item
-For Windows:
-@end itemize
+@menu
+* C Compiler for Windows::
+@end menu

-There are various ways to install one, depending on how you have installed
-Emacs. If you use Emacs within a Cygwin or MinGW environment, then you should
-install a compiler using their respective package manager.
+@node C Compiler for Windows
+@unnumberedsubsubsec C Compiler for Windows

-If you have installed your Emacs from the @uref{https://www.gnu.org/software/emacs/, GNU Emacs website}, then the easiest way
-is to use @uref{https://www.msys2.org/, MSYS2} as at the time of this writing:
+One of the easiest ways to install a C compiler in Windows is to use @uref{https://www.msys2.org/, MSYS2} as at the time of this writing:

@itemize
@item
-Use the installer in the official website and install MSYS2
+Download and use the installer in the official MSYS2 website

@item
-Run MSYS2
-
-@item
-In the command-line tool, type the following and answer ``Y'' to proceed:
+Run MSYS2 and in its terminal, type the following and answer ``Y'' to
+proceed -- this will install @code{gcc} in your PC:

@example
 pacman -S gcc
@end example

-Note that you do not need to manually set the PATH for MSYS2; the
-@end itemize
-installer automatically takes care of it for you.

-@itemize
@item
-Open Emacs and call @code{M-x org-roam-db-autosync-mode}
+On Windows, add @code{C:\msys64\usr\bin} (command @samp{where gcc} in MSYS2 terminal
+can tell you the correct path) to @code{PATH} in your environmental variables
+
+
+@item
+Launch Emacs and call @code{M-x org-roam-db-autosync-mode} (launch Emacs after
+defining the path, so that Emacs can recognize it)
+@end itemize

 This will automatically start compiling @code{emacsql-sqlite}; you should see a
-@end itemize
 message in minibuffer. It may take a while until compilation completes. Once
 complete, you should see a new file @code{emacsql-sqlite.exe} created in a subfolder
 named @code{sqlite} under @code{emacsql-sqlite} installation folder. It's typically in
@ -585,6 +589,7 @@ your Emacs configuration folder like this:
 * Links between Nodes::
 * Setting up Org-roam::
 * Creating and Linking Nodes::
+* Customizing Node Completions::
@end menu

@node The Org-roam Node
@ -651,7 +656,12 @@ For this tutorial, create an empty directory, and set @code{org-roam-directory}:
@end lisp

 The @code{file-truename} function is only necessary when you use symbolic links
-inside @code{org-roam-directory}: Org-roam does not resolve symbolic links.
+inside @code{org-roam-directory}: Org-roam does not resolve symbolic links. One can
+however instruct Emacs to always resolve symlinks, at a performance cost:
+
+@lisp
+(setq find-file-visit-truename t)
+@end lisp

 Next, we setup Org-roam to run functions on file changes to maintain cache
 consistency. This is achieved by running @code{M-x org-roam-db-autosync-mode}. To
@ -703,6 +713,56 @@ brought through the node creation process.
 One can also conveniently insert links via the completion-at-point functions
 Org-roam provides (see @ref{Completion}).

+@node Customizing Node Completions
+@section Customizing Node Completions
+
+Node selection is achieved via the @code{completing-read} interface, typically
+through `org-roam-node-read`. The presentation of these nodes are governed by
+@code{org-roam-node-display-template}.
+
+@defvar org-roam-node-display-template
+
+Configures display formatting for Org-roam node.
+
+Patterns of form ``$@{field-name:length@}'' are interpolated based
+on the current node.
+
+Each ``field-name'' is replaced with the return value of each
+corresponding accessor function for org-roam-node, e.g.
+``$@{title@}'' will be interpolated by the result of
+org-roam-node-title. You can also define custom accessors using
+cl-defmethod. For example, you can define:
+
+(cl-defmethod org-roam-node-my-title ((node org-roam-node))
+  (concat ``My '' (org-roam-node-title node)))
+
+and then reference it here or in the capture templates as
+``$@{my-title@}''.
+
+``length'' is an optional specifier and declares how many
+characters can be used to display the value of the corresponding
+field. If it's not specified, the field will be inserted as is,
+i.e. it won't be aligned nor trimmed. If it's an integer, the
+field will be aligned accordingly and all the exceeding
+characters will be trimmed out. If it's ``*'', the field will use
+as many characters as possible and will be aligned accordingly.
+
+A closure can also be assigned to this variable in which case the
+closure is evaluated and the return value is used as the
+template. The closure must evaluate to a valid template string.
+@end defvar
+
+If you're using a vertical completion framework, such as Ivy and Selectrum,
+Org-roam supports the generation of an aligned, tabular completion interface.
+For example, to include a column for tags up to 10 character widths wide, one
+can set @code{org-roam-node-display-template} as such:
+
+@lisp
+(setq org-roam-node-display-template
+      (concat "$@{title:*@} "
+              (propertize "$@{tags:10@}" 'face 'org-tag)))
+@end lisp
+
@node Customizing Node Caching
@chapter Customizing Node Caching

@ -785,6 +845,37 @@ all headlines with the @code{ATTACH} tag from the Org-roam database, one can set
        (not (member "ATTACH" (org-get-tags)))))
@end example

+Org-roam relied on the obtained Org AST for the buffer to parse links. However,
+links appearing in some places (e.g. within property drawers) are not considered
+by the Org AST to be links. Therefore, Org-roam takes special care of
+additionally trying to process these links. Use
+@code{org-roam-db-extra-links-elements} to specify which additional Org AST element
+types to consider.
+
+@defvar org-roam-db-extra-links-elements
+
+The list of Org element types to include for parsing by Org-roam.
+
+By default, when parsing Org's AST, links within keywords and
+property drawers are not parsed as links. Sometimes however, it
+is desirable to parse and cache these links (e.g. hiding links in
+a property drawer).
+@end defvar
+
+Additionally, one may want to ignore certain keys from being excluded within
+property drawers. For example, we would not want @code{ROAM_REFS} links to be
+self-referential. Hence, to exclude specific keys, we use
+@code{org-roam-db-extra-links-exclude-keys}.
+
+@defvar org-roam-db-extra-links-exclude-keys
+
+Keys to ignore when mapping over links.
+
+The car of the association list is the Org element type (e.g. keyword). The
+cdr is a list of case-insensitive strings to exclude from being treated as
+links.
+@end defvar
+
@node When to cache
@section When to cache

@ -886,10 +977,10 @@ There are currently 3 provided widget types:
 title/alias but are not linked
@end itemize

-To configure what sections are displayed in the buffer, set @code{org-roam-mode-section-functions}.
+To configure what sections are displayed in the buffer, set ~org-roam-mode-sections.

@lisp
-(setq org-roam-mode-section-functions
+(setq org-roam-mode-sections
      (list #'org-roam-backlinks-section
            #'org-roam-reflinks-section
            ;; #'org-roam-unlinked-references-section
@ -898,6 +989,16 @@ To configure what sections are displayed in the buffer, set @code{org-roam-mode-

 Note that computing unlinked references may be slow, and has not been added in by default.

+For each section function, you can pass args along to modify its behaviour. For
+example, if you want to render unique sources for backlinks (and also keep
+rendering reference links), set @code{org-roam-mode-sections} as follows:
+
+@lisp
+(setq org-roam-mode-sections
+      '((org-roam-backlinks-section :unique t)
+        org-roam-reflinks-section))
+@end lisp
+
@node Configuring the Org-roam buffer display
@section Configuring the Org-roam buffer display

@ -1041,7 +1142,7 @@ With the above example, if another node links to @uref{https://www.google.com/},
 will show up as a “reference backlink”.

 These keys also come in useful for when taking website notes, using the
- @code{roam-ref} protocol (see @ref{Org-roam Protocol, , Roam Protocol}).
+ @code{roam-ref} protocol (see @ref{org-roam-protocol}).

 You may assign multiple refs to a single node, for example when you want
 multiple papers in a series to share the same note, or an article has a citation
@ -1065,7 +1166,7 @@ Remove a ref from the node at point.

 Since version 9.5, Org has first-class support for citations. Org-roam supports
 the caching of both these in-built citations (of form @code{[cite:@@key]}) and @uref{https://github.com/jkitchin/org-ref, org-ref}
-citations (of form @uref{key}).
+citations (of form cite:key).

 Org-roam attempts to load both the @code{org-ref} and @code{org-cite} package when
 indexing files, so no further setup from the user is required for citation
@ -1090,6 +1191,16 @@ citation key:
 :END:
@end example

+or
+
+@example
+* Probabilistic Robotics
+:PROPERTIES:
+:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
+:ROAM_REFS: [cite:@@thrun2005probabilistic]
+:END:
+@end example
+
 for @code{org-cite}, or:

@example
@ -1185,243 +1296,6 @@ Note that the Org-roam database stores metadata information in plain-text
 (headline text, for example), so if this information is private to you then you
 should also ensure the database is encrypted.

-@node Org-roam Protocol
-@chapter Org-roam Protocol
-
-Org-roam provides extensions for capturing content from external applications
-such as the browser, via @code{org-protocol}. Org-roam extends @code{org-protocol} with 2
-protocols: the @code{roam-node} and @code{roam-ref} protocols.
-
-@menu
-* Installation: Installation (1). 
-* The roam-node protocol::
-* The roam-ref protocol::
-@end menu
-
-@node Installation (1)
-@section Installation
-
-To enable Org-roam's protocol extensions, simply add the following to your init
-file:
-
-@lisp
-(require 'org-roam-protocol)
-@end lisp
-
-We also need to set up @code{org-protocol}: the instructions for setting up
-@code{org-protocol} are reproduced below.
-
-@menu
-* Linux::
-* Mac OS::
-* Windows::
-@end menu
-
-@node Linux
-@subsection Linux
-
-For Linux users, create a desktop application in
-@code{~/.local/share/applications/org-protocol.desktop}:
-
-@example
-[Desktop Entry]
-Name=Org-Protocol
-Exec=emacsclient %u
-Icon=emacs-icon
-Type=Application
-Terminal=false
-MimeType=x-scheme-handler/org-protocol
-@end example
-
-Associate @code{org-protocol://} links with the desktop application by
-running in your shell:
-
-@example
-xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
-@end example
-
-To disable the ``confirm'' prompt in Chrome, you can also make Chrome show a
-checkbox to tick, so that the @code{Org-Protocol Client} app will be used without
-confirmation. To do this, run in a shell:
-
-@example
-sudo mkdir -p /etc/opt/chrome/policies/managed/
-sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
-@{
-  "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
-@}
-EOF
-sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
-@end example
-
-and then restart Chrome (for example, by navigating to <chrome://restart>) to
-make the new policy take effect.
-
-See @uref{https://www.chromium.org/administrators/linux-quick-start, here} for more info on the @code{/etc/opt/chrome/policies/managed} directory and
-@uref{https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox, here} for information on the @code{ExternalProtocolDialogShowAlwaysOpenCheckbox} policy.
-
-@node Mac OS
-@subsection Mac OS
-
-For Mac OS, we need to create our own application.
-
-@itemize
-@item
-Launch Script Editor
-
-@item
-Use the following script, paying attention to the path to @code{emacsclient}:
-@end itemize
-
-@lisp
-on open location this_URL
-    set EC to "/usr/local/bin/emacsclient --no-wait "
-    set filePath to quoted form of this_URL
-    do shell script EC & filePath
-    tell application "Emacs" to activate
-end open location
-@end lisp
-
-@itemize
-@item
-Save the script in @code{/Applications/OrgProtocolClient.app}, changing the script type to
-``Application'', rather than ``Script''.
-
-@item
-Edit @code{/Applications/OrgProtocolClient.app/Contents/Info.plist}, adding the
-following before the last @code{</dict>} tag:
-@end itemize
-
-@example
-<key>CFBundleURLTypes</key>
-<array>
-  <dict>
-    <key>CFBundleURLName</key>
-    <string>org-protocol handler</string>
-    <key>CFBundleURLSchemes</key>
-    <array>
-      <string>org-protocol</string>
-    </array>
-  </dict>
-</array>
-@end example
-
-@itemize
-@item
-Save the file, and run the @code{OrgProtocolClient.app} to register the protocol.
-@end itemize
-
-To disable the ``confirm'' prompt in Chrome, you can also make Chrome
-show a checkbox to tick, so that the @code{OrgProtocol} app will be used
-without confirmation. To do this, run in a shell:
-
-@example
-defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
-@end example
-
-If you're using @uref{https://github.com/railwaycat/homebrew-emacsmacport, Emacs Mac Port}, it registered its `Emacs.app` as the default
-handler for the URL scheme `org-protocol`. To make @code{OrgProtocol.app}
-the default handler instead, run:
-
-@example
-defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
-'@{"LSHandlerPreferredVersions" = @{ "LSHandlerRoleAll" = "-"; @}; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";@}'
-@end example
-
-Then restart your computer.
-
-@menu
-* Testing org-protocol::
-@end menu
-
-@node Testing org-protocol
-@unnumberedsubsubsec Testing org-protocol
-
-To test that you have the handler setup and registered properly from the command
-line you can run:
-
-@example
-open org-protocol://roam-ref\?template=r\&ref=test\&title=this
-@end example
-
-If you get an error similar too this or the wrong handler is run:
-
-@quotation
-No application knows how to open URL org-protocol://roam-ref?template=r&ref=test&title=this (Error Domain=NSOSStatusErrorDomain Code=-10814 ``kLSApplicationNotFoundErr: E.g. no application claims the file'' UserInfo=@{@math{_LSLine}=1489, _LSFunction=runEvaluator@}).
-
-@end quotation
-
-You may need to manually register your handler, like this:
-
-@example
-/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
-@end example
-
-Here is a link to the lsregister command that is really useful: @uref{https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/}
-
-@node Windows
-@subsection Windows
-
-For Windows, create a temporary @code{org-protocol.reg} file:
-
-@example
-REGEDIT4
-
-[HKEY_CLASSES_ROOT\org-protocol]
-@@="URL:Org Protocol"
-"URL Protocol"=""
-[HKEY_CLASSES_ROOT\org-protocol\shell]
-[HKEY_CLASSES_ROOT\org-protocol\shell\open]
-[HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
-@@="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""
-@end example
-
-The above will forward the protocol to WSL@. If you run Emacs natively on
-Windows, replace the last line with:
-
-@example
-@@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
-@end example
-
-After executing the .reg file, the protocol is registered and you can delete the
-file.
-
-@node The roam-node protocol
-@section The roam-node protocol
-
-The roam-node protocol opens the node with ID specified by the @code{node} key (e.g.
-@code{org-protocol://roam-node?node=node-id}). @code{org-roam-graph} uses this to make the
-graph navigable.
-
-@node The roam-ref protocol
-@section The roam-ref protocol
-
-This protocol finds or creates a new note with a given @code{ROAM_REFS}:
-
-@image{images/roam-ref,,,,gif}
-
-To use this, create the following @uref{https://en.wikipedia.org/wiki/Bookmarklet, bookmarklet} in your browser:
-
-@example
-javascript:location.href =
-    'org-protocol://roam-ref?template=r&ref='
-    + encodeURIComponent(location.href)
-    + '&title='
-    + encodeURIComponent(document.title)
-    + '&body='
-    + encodeURIComponent(window.getSelection())
-@end example
-
-or as a keybinding in @code{qutebrowser} in , using the @code{config.py} file (see
-@uref{https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc, Configuring qutebrowser}):
-
-@example
-config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)")
-@end example
-
-where @code{template} is the template key for a template in
-@code{org-roam-capture-ref-templates} (see @ref{The Templating System}).
-
@node The Templating System
@chapter The Templating System

@ -1538,13 +1412,272 @@ One can check the list of available keys for nodes by inspecting the

 This makes @code{$@{file@}}, @code{$@{file-hash@}} etc. all valid substitutions.

-@node Graphing
-@chapter Graphing
+@node Extensions
+@chapter Extensions
+
+@menu
+* org-roam-protocol::
+* org-roam-graph::
+* org-roam-dailies::
+* org-roam-export::
+@end menu
+
+@node org-roam-protocol
+@section org-roam-protocol
+
+Org-roam provides extensions for capturing content from external applications
+such as the browser, via @code{org-protocol}. Org-roam extends @code{org-protocol} with 2
+protocols: the @code{roam-node} and @code{roam-ref} protocols.
+
+@menu
+* Installation: Installation (1). 
+* The roam-node protocol::
+* The roam-ref protocol::
+@end menu
+
+@node Installation (1)
+@subsection Installation
+
+To enable Org-roam's protocol extensions, simply add the following to your init
+file:
+
+@lisp
+(require 'org-roam-protocol)
+@end lisp
+
+We also need to set up @code{org-protocol}: the instructions for setting up
+@code{org-protocol} are reproduced here.
+
+On a high-level, external calls are passed to Emacs via @code{emacsclient}.
+@code{org-protocol} intercepts these and runs custom actions based on the protocols
+registered. Hence, to use @code{org-protocol}, once must:
+
+@itemize
+@item
+launch the @code{emacsclient} process
+
+@item
+Register @code{org-protocol://} as a valid scheme-handler
+@end itemize
+
+The instructions for the latter for each operating system is detailed below.
+
+@menu
+* Linux::
+* Mac OS::
+* Windows::
+@end menu
+
+@node Linux
+@unnumberedsubsubsec Linux
+
+For Linux users, create a desktop application in
+@code{~/.local/share/applications/org-protocol.desktop}:
+
+@example
+[Desktop Entry]
+Name=Org-Protocol
+Exec=emacsclient %u
+Icon=emacs-icon
+Type=Application
+Terminal=false
+MimeType=x-scheme-handler/org-protocol
+@end example
+
+Associate @code{org-protocol://} links with the desktop application by
+running in your shell:
+
+@example
+xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
+@end example
+
+To disable the ``confirm'' prompt in Chrome, you can also make Chrome show a
+checkbox to tick, so that the @code{Org-Protocol Client} app will be used without
+confirmation. To do this, run in a shell:
+
+@example
+sudo mkdir -p /etc/opt/chrome/policies/managed/
+sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
+@{
+  "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
+@}
+EOF
+sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
+@end example
+
+and then restart Chrome (for example, by navigating to <chrome://restart>) to
+make the new policy take effect.
+
+See @uref{https://www.chromium.org/administrators/linux-quick-start, here} for more info on the @code{/etc/opt/chrome/policies/managed} directory and
+@uref{https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox, here} for information on the @code{ExternalProtocolDialogShowAlwaysOpenCheckbox} policy.
+
+@node Mac OS
+@unnumberedsubsubsec Mac OS
+
+For Mac OS, we need to create our own application.
+
+@itemize
+@item
+Launch Script Editor
+
+@item
+Use the following script, paying attention to the path to @code{emacsclient}:
+@end itemize
+
+@lisp
+on open location this_URL
+    set EC to "/usr/local/bin/emacsclient --no-wait "
+    set filePath to quoted form of this_URL
+    do shell script EC & filePath
+    tell application "Emacs" to activate
+end open location
+@end lisp
+
+@itemize
+@item
+Save the script in @code{/Applications/OrgProtocolClient.app}, changing the script type to
+``Application'', rather than ``Script''.
+
+@item
+Edit @code{/Applications/OrgProtocolClient.app/Contents/Info.plist}, adding the
+following before the last @code{</dict>} tag:
+@end itemize
+
+@example
+<key>CFBundleURLTypes</key>
+<array>
+  <dict>
+    <key>CFBundleURLName</key>
+    <string>org-protocol handler</string>
+    <key>CFBundleURLSchemes</key>
+    <array>
+      <string>org-protocol</string>
+    </array>
+  </dict>
+</array>
+@end example
+
+@itemize
+@item
+Save the file, and run the @code{OrgProtocolClient.app} to register the protocol.
+@end itemize
+
+To disable the ``confirm'' prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the @code{OrgProtocol} app will be used
+without confirmation. To do this, run in a shell:
+
+@example
+defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
+@end example
+
+If you're using @uref{https://github.com/railwaycat/homebrew-emacsmacport, Emacs Mac Port}, it registered its `Emacs.app` as the default
+handler for the URL scheme `org-protocol`. To make @code{OrgProtocol.app}
+the default handler instead, run:
+
+@example
+defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
+'@{"LSHandlerPreferredVersions" = @{ "LSHandlerRoleAll" = "-"; @}; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";@}'
+@end example
+
+Then restart your computer.
+
+@itemize
+@item
+@anchor{Testing org-protocol}Testing org-protocol
+
+
+To test that you have the handler setup and registered properly from the command
+line you can run:
+
+@example
+open org-protocol://roam-ref\?template=r\&ref=test\&title=this
+@end example
+
+If you get an error similar too this or the wrong handler is run:
+
+@quotation
+No application knows how to open URL org-protocol://roam-ref?template=r&ref=test&title=this (Error Domain=NSOSStatusErrorDomain Code=-10814 ``kLSApplicationNotFoundErr: E.g. no application claims the file'' UserInfo=@{@math{_LSLine}=1489, _LSFunction=runEvaluator@}).
+
+@end quotation
+
+You may need to manually register your handler, like this:
+
+@example
+/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
+@end example
+
+Here is a link to the lsregister command that is really useful: @uref{https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/}
+@end itemize
+
+@node Windows
+@unnumberedsubsubsec Windows
+
+For Windows, create a temporary @code{org-protocol.reg} file:
+
+@example
+REGEDIT4
+
+[HKEY_CLASSES_ROOT\org-protocol]
+@@="URL:Org Protocol"
+"URL Protocol"=""
+[HKEY_CLASSES_ROOT\org-protocol\shell]
+[HKEY_CLASSES_ROOT\org-protocol\shell\open]
+[HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
+@@="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""
+@end example
+
+The above will forward the protocol to WSL@. If you run Emacs natively on
+Windows, replace the last line with:
+
+@example
+@@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
+@end example
+
+After executing the .reg file, the protocol is registered and you can delete the
+file.
+
+@node The roam-node protocol
+@subsection The roam-node protocol
+
+The roam-node protocol opens the node with ID specified by the @code{node} key (e.g.
+@code{org-protocol://roam-node?node=node-id}). @code{org-roam-graph} uses this to make the
+graph navigable.
+
+@node The roam-ref protocol
+@subsection The roam-ref protocol
+
+This protocol finds or creates a new note with a given @code{ROAM_REFS}:
+
+@image{images/roam-ref,,,,gif}
+
+To use this, create the following @uref{https://en.wikipedia.org/wiki/Bookmarklet, bookmarklet} in your browser:
+
+@example
+javascript:location.href =
+    'org-protocol://roam-ref?template=r&ref='
+    + encodeURIComponent(location.href)
+    + '&title='
+    + encodeURIComponent(document.title)
+    + '&body='
+    + encodeURIComponent(window.getSelection())
+@end example
+
+or as a keybinding in @code{qutebrowser} in , using the @code{config.py} file (see
+@uref{https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc, Configuring qutebrowser}):
+
+@example
+config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)")
+@end example
+
+where @code{template} is the template key for a template in
+@code{org-roam-capture-ref-templates} (see @ref{The Templating System}).
+
+@node org-roam-graph
+@section org-roam-graph

 Org-roam provides basic graphing capabilities to explore interconnections
 between notes, in @code{org-roam-graph}. This is done by performing SQL queries and
-generating images using @uref{https://graphviz.org/, Graphviz}. The graph can also be navigated: see @ref{Org-roam Protocol, , Roam
-Protocol}.
+generating images using @uref{https://graphviz.org/, Graphviz}. The graph can also be navigated: see @ref{org-roam-protocol}.

 The entry point to graph creation is @code{org-roam-graph}.

@ -1602,7 +1735,7 @@ the second option to set the browser and network file path:
@end menu

@node Graph Options
-@section Graph Options
+@subsection Graph Options

 Graphviz provides many options for customizing the graph output, and Org-roam
 supports some of them. See @uref{https://graphviz.gitlab.io/_pages/doc/info/attrs.html}
@ -1632,8 +1765,8 @@ Extra options for edges in the graphviz output (The ``E'' attributes).
 Example: @code{'(("dir" . "back"))}
@end defopt

-@node Org-roam Dailies
-@chapter Org-roam Dailies
+@node org-roam-dailies
+@section org-roam-dailies

 Org-roam provides journaling capabilities akin to
 Org-journal with @code{org-roam-dailies}.
@ -1644,7 +1777,7 @@ Org-journal with @code{org-roam-dailies}.
@end menu

@node Configuration
-@section Configuration
+@subsection Configuration

 For @code{org-roam-dailies} to work, you need to define two variables:

@ -1673,7 +1806,7 @@ Here is a sane default configuration:
 See @ref{The Templating System} for creating new templates.

@node Usage
-@section Usage
+@subsection Usage

@code{org-roam-dailies} provides these interactive functions:

@ -1737,6 +1870,19 @@ When in an daily-note, find the previous one.
 When in an daily-note, find the next one.
@end defun

+@node org-roam-export
+@section org-roam-export
+
+Because Org-roam files are plain org files, they can be exported easily using
+@code{org-export} to a variety of formats, including @code{html} and @code{pdf}. However,
+Org-roam relies heavily on ID links, which Org's html export has poor support
+of. To fix this, Org-roam provides a bunch of overrides to better support
+export. To use them, simply run:
+
+@lisp
+(require 'org-roam-export)
+@end lisp
+
@node Performance Optimization
@chapter Performance Optimization

@ -1834,7 +1980,7 @@ The Deft interface can slow down quickly when the number of files get huge.

@uref{https://github.com/bastibe/org-journal, Org-journal} provides journaling capabilities to Org-mode. A lot of its
 functionalities have been incorporated into Org-roam under the name
-@ref{Org-roam Dailies, , @code{org-roam-dailies}}. It remains a good tool if you want to isolate your verbose
+@ref{org-roam-dailies, , @code{org-roam-dailies}}. It remains a good tool if you want to isolate your verbose
 journal entries from the ideas you would write on a scratchpad.

@lisp
@ -1895,6 +2041,9 @@ documents (PDF, EPUB etc.) within Org-mode.
@node Bibliography
@section Bibliography

+Org 9.5 added native citation and bibliography functionality, called ``org-cite'',
+which org-roam supports.
+
@uref{https://github.com/org-roam/org-roam-bibtex, org-roam-bibtex} offers tight integration between @uref{https://github.com/jkitchin/org-ref, org-ref}, @uref{https://github.com/tmalsburg/helm-bibtex, helm-bibtex} and
@code{org-roam}. This helps you manage your bibliographic notes under @code{org-roam}.

@ -1921,6 +2070,7 @@ Org-mode, and sync your cards to Anki via @uref{https://github.com/FooSoft/anki-
 * How do I migrate from Roam Research?::
 * How to migrate from Org-roam v1?::
 * How do I publish my notes with an Internet-friendly graph?::
+* I'm seeing this ``Selecting deleted buffer'' error. What do I do?: I'm seeing this ``Selecting deleted buffer'' error What do I do?. 
@end menu

@node How do I have more than one Org-roam directory?
@ -2131,6 +2281,27 @@ to the publishing directory.  Example code follows:
                                       (setq my-publish-time 0)))))
@end lisp

+@node I'm seeing this ``Selecting deleted buffer'' error What do I do?
+@section I'm seeing this ``Selecting deleted buffer'' error. What do I do?
+
+The ``selecting deleted buffer'' error usually occurs when you don't have a
+working @code{emacsql-sqlite} executable. Org-roam relies on this executable to
+function properly, and doesn't catch this error. This issue is most commonly
+seen on Windows setups. You can browse through the various GitHub issues posted
+about this @uref{https://github.com/org-roam/org-roam/issues?q=is%3Aissue+selecting+deleted, here}.
+
+To fix this, you can try the following:
+
+@itemize
+@item
+If on Windows, try replacing your system binary with @uref{https://github.com/nobiot/emacsql-sqlite.exe, this one} that has been proven
+to work
+
+@item
+Use the @code{emacsql-sqlite3} option rather than compiling your own emacsql
+binary (see @ref{How to cache}).
+@end itemize
+
@node Developer's Guide to Org-roam
@chapter Developer's Guide to Org-roam

--- a/extensions/org-roam-dailies.el
+++ b/extensions/org-roam-dailies.el
@ -1,14 +1,14 @@
 ;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
 ;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;;      Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org-roam "2.1"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org-roam "2.1"))

 ;; This file is NOT part of GNU Emacs.

@ -34,10 +34,9 @@
 ;; each file named after certain date and stored in `org-roam-dailies-directory'.
 ;;
 ;; One can use dailies for various purposes, e.g. journaling, fleeting notes,
-;; scratch notes and whatever else you can came up with.
+;; scratch notes or whatever else you can think of.
 ;;
 ;;; Code:
-(require 'f)
 (require 'dash)
 (require 'org-roam)

@ -130,79 +129,103 @@ See `org-roam-capture-templates' for the template documentation."
 ;;; Commands
 ;;;; Today
 ;;;###autoload
-(defun org-roam-dailies-capture-today (&optional goto)
+(defun org-roam-dailies-capture-today (&optional goto keys)
  "Create an entry in the daily-note for today.
-When GOTO is non-nil, go the note without creating an entry."
+When GOTO is non-nil, go the note without creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive "P")
-  (org-roam-dailies--capture (current-time) goto))
+  (org-roam-dailies--capture (current-time) goto keys))

 ;;;###autoload
-(defun org-roam-dailies-goto-today ()
-  "Find the daily-note for today, creating it if necessary."
+(defun org-roam-dailies-goto-today (&optional keys)
+  "Find the daily-note for today, creating it if necessary.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive)
-  (org-roam-dailies-capture-today t))
+  (org-roam-dailies-capture-today t keys))

 ;;;; Tomorrow
 ;;;###autoload
-(defun org-roam-dailies-capture-tomorrow (n &optional goto)
+(defun org-roam-dailies-capture-tomorrow (n &optional goto keys)
  "Create an entry in the daily-note for tomorrow.

 With numeric argument N, use the daily-note N days in the future.

 With a `C-u' prefix or when GOTO is non-nil, go the note without
-creating an entry."
+creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive "p")
-  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto keys))

 ;;;###autoload
-(defun org-roam-dailies-goto-tomorrow (n)
+(defun org-roam-dailies-goto-tomorrow (n &optional keys)
  "Find the daily-note for tomorrow, creating it if necessary.

 With numeric argument N, use the daily-note N days in the
-future."
+future.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive "p")
-  (org-roam-dailies-capture-tomorrow n t))
+  (org-roam-dailies-capture-tomorrow n t keys))

 ;;;; Yesterday
 ;;;###autoload
-(defun org-roam-dailies-capture-yesterday (n &optional goto)
+(defun org-roam-dailies-capture-yesterday (n &optional goto keys)
  "Create an entry in the daily-note for yesteday.

 With numeric argument N, use the daily-note N days in the past.

-When GOTO is non-nil, go the note without creating an entry."
+When GOTO is non-nil, go the note without creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) goto))
+  (org-roam-dailies-capture-tomorrow (- n) goto keys))

 ;;;###autoload
-(defun org-roam-dailies-goto-yesterday (n)
+(defun org-roam-dailies-goto-yesterday (n &optional keys)
  "Find the daily-note for yesterday, creating it if necessary.

 With numeric argument N, use the daily-note N days in the
-future."
+future.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) t))
+  (org-roam-dailies-capture-tomorrow (- n) t keys))

 ;;;; Date
 ;;;###autoload
-(defun org-roam-dailies-capture-date (&optional goto prefer-future)
+(defun org-roam-dailies-capture-date (&optional goto prefer-future keys)
  "Create an entry in the daily-note for a date using the calendar.
 Prefer past dates, unless PREFER-FUTURE is non-nil.
 With a `C-u' prefix or when GOTO is non-nil, go the note without
-creating an entry."
+creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive "P")
  (let ((time (let ((org-read-date-prefer-future prefer-future))
                (org-read-date nil t nil (if goto
                                             "Find daily-note: "
                                           "Capture to daily-note: ")))))
-    (org-roam-dailies--capture time goto)))
+    (org-roam-dailies--capture time goto keys)))

 ;;;###autoload
-(defun org-roam-dailies-goto-date (&optional prefer-future)
+(defun org-roam-dailies-goto-date (&optional prefer-future keys)
  "Find the daily-note for a date using the calendar, creating it if necessary.
-Prefer past dates, unless PREFER-FUTURE is non-nil."
+Prefer past dates, unless PREFER-FUTURE is non-nil.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
  (interactive)
-  (org-roam-dailies-capture-date t prefer-future))
+  (org-roam-dailies-capture-date t prefer-future keys))

 ;;;; Navigation
 (defun org-roam-dailies-goto-next-note (&optional n)
@ -266,7 +289,7 @@ If FILE is not specified, use the current buffer's file-path."
    (save-match-data
      (and
       (org-roam-file-p path)
-       (f-descendant-of-p path directory)))))
+       (org-roam-descendant-of-p path directory)))))

 ;;;###autoload
 (defun org-roam-dailies-find-directory ()
@ -300,11 +323,16 @@ Return (MONTH DAY YEAR) or nil if not an Org time-string."
 ;;; Capture implementation
 (add-to-list 'org-roam-capture--template-keywords :override-default-time)

-(defun org-roam-dailies--capture (time &optional goto)
+(defun org-roam-dailies--capture (time &optional goto keys)
  "Capture an entry in a daily-note for TIME, creating it if necessary.
-When GOTO is non-nil, go the note without creating an entry."
-  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
+When GOTO is non-nil, go the note without creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
+  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory))
+        (org-roam-dailies-directory "./"))
    (org-roam-capture- :goto (when goto '(4))
+                       :keys keys
                       :node (org-roam-node-create)
                       :templates org-roam-dailies-capture-templates
                       :props (list :override-default-time time)))
--- a/extensions/org-roam-export.el
+++ b/extensions/org-roam-export.el
@ -0,0 +1,75 @@
+;;; org-roam-export.el --- Org-roam org-export tweaks -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This package provides the necessary changes required to make org-export work out-of-the-box.
+;;
+;; To enable it, run:
+;;
+;;    (require 'org-roam-export)
+;;
+;; The key issue Org's export-to-html functionality has is that it does not respect the ID property, which
+;; Org-roam relies heavily on. This patches the necessary function in ox-html to export ID links correctly,
+;; pointing to the correct place.
+;;
+;;; Code:
+(require 'ox-html)
+
+(defun org-roam-export--org-html--reference (datum info &optional named-only)
+  "Org-roam's patch for `org-html--reference' to support ID link export.
+See `org-html--reference' for DATUM, INFO and NAMED-ONLY."
+  (let* ((type (org-element-type datum))
+         (user-label
+          (org-element-property
+           (pcase type
+             ((or `headline `inlinetask) :CUSTOM_ID)
+             ((or `radio-target `target) :value)
+             (_ :name))
+           datum))
+         (user-label
+          (or user-label
+              (when-let ((path (org-element-property :ID datum)))
+                ;; see `org-html-link' for why we use "ID-"
+                ;; (search for "ID-" in ox-html.el)
+                (concat "ID-" path)))))
+    (cond
+     ((and user-label
+           (or (plist-get info :html-prefer-user-labels)
+               (memq type '(headline inlinetask))))
+      user-label)
+     ((and named-only
+           (not (memq type '(headline inlinetask radio-target target)))
+           (not user-label))
+      nil)
+     (t
+      (org-export-get-reference datum info)))))
+
+(advice-add 'org-html--reference :override #'org-roam-export--org-html--reference)
+
+(provide 'org-roam-export)
+;;; org-roam-export.el ends here
--- a/extensions/org-roam-graph.el
+++ b/extensions/org-roam-graph.el
@ -1,11 +1,11 @@
 ;;; org-roam-graph.el --- Basic graphing functionality for Org-roam -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
+;; Version: 2.2.1
 ;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))

 ;; This file is NOT part of GNU Emacs.
@ -266,7 +266,7 @@ Handles both Org-roam nodes, and string nodes (e.g. urls)."
                (org-roam-quote-string
                 (pcase org-roam-graph-shorten-titles
                   (`truncate (truncate-string-to-width title org-roam-graph-max-title-length nil nil "..."))
-                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                   (`wrap (org-roam-word-wrap org-roam-graph-max-title-length title))
                   (_ title)))))
          (setq node-id (org-roam-node-id node)
                node-properties `(("label"   . ,shortened-title)
--- a/extensions/org-roam-overlay.el
+++ b/extensions/org-roam-overlay.el
@ -1,11 +1,11 @@
 ;;; org-roam-overlay.el --- Link overlay for [id:] links to Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
+;; Version: 2.2.1
 ;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))

 ;; This file is NOT part of GNU Emacs.
--- a/extensions/org-roam-protocol.el
+++ b/extensions/org-roam-protocol.el
@ -1,10 +1,10 @@
 ;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
+;; Version: 2.2.1
 ;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))

 ;; This file is NOT part of GNU Emacs.
@ -169,25 +169,6 @@ org-protocol://roam-node?node=uuid"
 (push '("org-roam-node"  :protocol "roam-node"   :function org-roam-protocol-open-node)
      org-protocol-protocol-alist)

-;;; Capture implementation
-(add-hook 'org-roam-capture-preface-hook #'org-roam-protocol--try-capture-to-ref-h)
-(defun org-roam-protocol--try-capture-to-ref-h ()
-  "Try to capture to an existing node that match the ref."
-  (when-let ((node (and (plist-get org-roam-capture--info :ref)
-                        (org-roam-node-from-ref
-                         (plist-get org-roam-capture--info :ref)))))
-    (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
-    (goto-char (org-roam-node-point node))
-    (widen)
-    (org-roam-node-id node)))
-
-(add-hook 'org-roam-capture-new-node-hook #'org-roam-protocol--insert-captured-ref-h)
-(defun org-roam-protocol--insert-captured-ref-h ()
-  "Insert the ref if any."
-  (when-let ((ref (plist-get org-roam-capture--info :ref)))
-    (org-roam-ref-add ref)))
-
-
 (provide 'org-roam-protocol)

 ;;; org-roam-protocol.el ends here
--- a/11
+++ b/11
@ -0,0 +1,11 @@
+#! /bin/sh
+set -e
+
+ELDEV_BIN_DIR=~/.local/bin
+
+# `$GITHUB_PATH' is a magic file which contents is translated to environment variable `$PATH'.
+echo "$ELDEV_BIN_DIR" >> $GITHUB_PATH
+
+mkdir -p $ELDEV_BIN_DIR
+curl -fsSL https://raw.githubusercontent.com/doublep/eldev/f111d19cda305e5e8fcb70a5675b87173041cb68/bin/eldev > $ELDEV_BIN_DIR/eldev
+chmod a+x $ELDEV_BIN_DIR/eldev
--- a/org-roam-capture.el
+++ b/org-roam-capture.el
@ -1,12 +1,12 @@
 ;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))

 ;; This file is NOT part of GNU Emacs.

@ -407,6 +407,8 @@ TEMPLATES is a list of org-roam templates."
          (mapcar (lambda (template)
                    (org-roam-capture--convert-template template props))
                  (or templates org-roam-capture-templates)))
+         (_ (setf (org-roam-node-id node) (or (org-roam-node-id node)
+                                              (org-id-new))))
         (org-roam-capture--node node)
         (org-roam-capture--info info))
    (when (and (not keys)
@ -503,7 +505,7 @@ Return the ID of the location."
       (set-buffer (org-capture-target-buffer path))
       (when new-file-p
         (org-roam-capture--put :new-file path)
-         (insert (org-roam-capture--fill-template head t)))
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
       (widen)
       (setq p (goto-char (point-min))))
      (`(file+head+olp ,path ,head ,olp)
@ -513,7 +515,7 @@ Return the ID of the location."
       (widen)
       (when new-file-p
         (org-roam-capture--put :new-file path)
-         (insert (org-roam-capture--fill-template head t)))
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
       (setq p (point-min))
       (let ((m (org-roam-capture-find-or-create-olp olp)))
         (goto-char m)))
@ -572,11 +574,11 @@ Return the ID of the location."
    ;; caller.
    (save-excursion
      (goto-char p)
-      (when-let* ((node org-roam-capture--node)
-                  (id (org-roam-node-id node)))
-        (org-entry-put p "ID" id))
+      (if-let ((id (org-entry-get p "ID")))
+          (setf (org-roam-node-id org-roam-capture--node) id)
+        (org-entry-put p "ID" (org-roam-node-id org-roam-capture--node)))
      (prog1
-          (org-id-get-create)
+          (org-id-get)
        (run-hooks 'org-roam-capture-new-node-hook)))))

 (defun org-roam-capture--get-target ()
@ -589,8 +591,9 @@ Return the ID of the location."
 PATH is a string that can optionally contain templated text in
 it."
  (or (org-roam-node-file org-roam-capture--node)
-      (thread-first path
-        (org-roam-capture--fill-template t)
+      (thread-first
+        path
+        (org-roam-capture--fill-template)
        (string-trim)
        (expand-file-name org-roam-directory))))

@ -615,7 +618,7 @@ you can catch it with `condition-case'."
    (org-with-wide-buffer
     (goto-char start)
     (dolist (heading olp)
-       (setq heading (org-roam-capture--fill-template heading t))
+       (setq heading (org-roam-capture--fill-template heading))
       (let ((re (format org-complex-heading-regexp-format
                         (regexp-quote heading)))
             (cnt 0))
@ -677,6 +680,24 @@ the current value of `point'."
            (goto-char (org-entry-end-position))))))))
  (point))

+;;; Capture implementation
+(add-hook 'org-roam-capture-preface-hook #'org-roam-capture--try-capture-to-ref-h)
+(defun org-roam-capture--try-capture-to-ref-h ()
+  "Try to capture to an existing node that match the ref."
+  (when-let ((node (and (plist-get org-roam-capture--info :ref)
+                        (org-roam-node-from-ref
+                         (plist-get org-roam-capture--info :ref)))))
+    (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
+    (goto-char (org-roam-node-point node))
+    (widen)
+    (org-roam-node-id node)))
+
+(add-hook 'org-roam-capture-new-node-hook #'org-roam-capture--insert-captured-ref-h)
+(defun org-roam-capture--insert-captured-ref-h ()
+  "Insert the ref if any."
+  (when-let ((ref (plist-get org-roam-capture--info :ref)))
+    (org-roam-ref-add ref)))
+
 ;;;; Finalizers
 (add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize-h)
 (defun org-roam-capture--install-finalize-h ()
@ -689,11 +710,14 @@ the current value of `point'."
  (when-let ((region (org-roam-capture--get :region)))
    (org-roam-unshield-region (car region) (cdr region)))
  (if org-note-abort
-      (when-let ((new-file (org-roam-capture--get :new-file)))
-        (org-roam-message "Deleting file for aborted capture %s" new-file)
+      (when-let ((new-file (org-roam-capture--get :new-file))
+                 (_ (yes-or-no-p "Delete file for aborted capture?")))
        (when (find-buffer-visiting new-file)
          (kill-buffer (find-buffer-visiting new-file)))
        (delete-file new-file))
+    (when-let* ((buffer (plist-get org-capture-plist :buffer))
+                (file (buffer-file-name buffer)))
+      (org-id-add-location (org-roam-capture--get :id) file))
    (when-let* ((finalize (org-roam-capture--get :finalize))
                (org-roam-finalize-fn (intern (concat "org-roam-capture--finalize-"
                                                      (symbol-name finalize)))))
@ -720,48 +744,56 @@ This function is to be called in the Org-capture finalization process."
        (delete-region (car region) (cdr region))
        (set-marker (car region) nil)
        (set-marker (cdr region) nil))
-      (org-with-point-at mkr
-        (insert (org-link-make-string (concat "id:" (org-roam-capture--get :id))
-                                      (org-roam-capture--get :link-description)))))))
+      (let* ((id (org-roam-capture--get :id))
+             (description (org-roam-capture--get :link-description))
+             (link (org-link-make-string (concat "id:" id)
+                                         description)))
+        (if (eq (point) (marker-position mkr))
+            (insert link)
+          (org-with-point-at mkr
+            (insert link)))
+        (run-hook-with-args 'org-roam-post-node-insert-hook
+                            id
+                            description)))))

 ;;;; Processing of the capture templates
-(defun org-roam-capture--fill-template (template &optional org-capture-p newline)
+(defun org-roam-capture--fill-template (template &optional ensure-newline)
  "Expand TEMPLATE and return it.
-It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
-also run Org-capture's template expansion.
-If NEWLINE, ensure that the template returned ends with a newline."
-  (setq template (org-roam-format-template
-                  template
-                  (lambda (key default-val)
-                    (let ((fn (intern key))
-                          (node-fn (intern (concat "org-roam-node-" key)))
-                          (ksym (intern (concat ":" key))))
-                      (cond
-                       ((fboundp fn)
-                        (funcall fn org-roam-capture--node))
-                       ((fboundp node-fn)
-                        (funcall node-fn org-roam-capture--node))
-                       ((plist-get org-roam-capture--info ksym)
-                        (plist-get org-roam-capture--info ksym))
-                       (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
-                            (plist-put org-roam-capture--info ksym r)
-                            r)))))))
-  ;; WARNING:
-  ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
-  ;; template does not start with any whitespace, and only ends with a single newline
-  ;;
-  ;; In most cases where we rely on `org-capture-fill-template' to populate non-org-capture-related templates,
-  ;; (e.g. in OLPs), we strip the final newline, obtaining a template that seems to be string-trimmed.
-  ;;
-  ;; This means that if the original passed template has newlines, and ORG-CAPTURE-P is true, then the extra
-  ;; whitespace specified in the template will be ignored.
-  (when org-capture-p
+It expands ${var} occurrences in TEMPLATE, and then runs
+org-capture's template expansion.
+When ENSURE-NEWLINE, always ensure there's a newline behind."
+  (let* ((template (if (functionp template)
+                       (funcall template)
+                     template))
+         (template-whitespace-content (org-roam-whitespace-content template)))
    (setq template
-          (replace-regexp-in-string "\n$" "" (org-capture-fill-template template))))
-  (when (and newline
-             (not (string-suffix-p "\n" template)))
-    (setq template (concat template "\n")))
-  template)
+          (org-roam-format-template
+           template
+           (lambda (key default-val)
+             (let ((fn (intern key))
+                   (node-fn (intern (concat "org-roam-node-" key)))
+                   (ksym (intern (concat ":" key))))
+               (cond
+                ((fboundp fn)
+                 (funcall fn org-roam-capture--node))
+                ((fboundp node-fn)
+                 (funcall node-fn org-roam-capture--node))
+                ((plist-get org-roam-capture--info ksym)
+                 (plist-get org-roam-capture--info ksym))
+                (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
+                     (plist-put org-roam-capture--info ksym r)
+                     r)))))))
+    ;; WARNING:
+    ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
+    ;; template does not start with any whitespace, and only ends with a single newline
+    ;;
+    ;; Instead, we restore the whitespace in the original template.
+    (setq template (replace-regexp-in-string "\n$" "" (org-capture-fill-template template)))
+    (when (and ensure-newline
+               (string-equal template-whitespace-content ""))
+      (setq template-whitespace-content "\n"))
+    (setq template (concat template template-whitespace-content))
+    template))

 (defun org-roam-capture--convert-template (template &optional props)
  "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax.
--- a/org-roam-compat.el
+++ b/org-roam-compat.el
@ -1,11 +1,11 @@
 ;;; org-roam-compat.el --- Backward compatibility code -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
+;; Version: 2.2.1
 ;; Package-Requires: ((emacs "26.1"))

 ;; This file is NOT part of GNU Emacs.
@ -229,6 +229,10 @@ nodes." org-id-locations-file)
  'org-roam-remove-property
  'org-roam-property-remove "org-roam 2.1")

+(define-obsolete-variable-alias
+  'org-roam-mode-section-functions
+  'org-roam-mode-sections "org-roam 2.2.0")
+
 ;;; Obsolete functions
 (make-obsolete 'org-roam-get-keyword 'org-collect-keywords "org-roam 2.0")

--- a/org-roam-db.el
+++ b/org-roam-db.el
@ -1,12 +1,12 @@
 ;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))

 ;; This file is NOT part of GNU Emacs.

@ -36,25 +36,37 @@
 ;;; Options
 (defcustom org-roam-database-connector 'sqlite
  "The database connector used by Org-roam.
-This must be set before `org-roam' is loaded. To use an
-alternative connector you must install the respective package
-explicitly. When `sqlite', then use the `emacsql-sqlite' library
+This must be set before `org-roam' is loaded.  To use an alternative
+connector you must install the respective package explicitly.
+The default is `sqlite', which uses the `emacsql-sqlite' library
 that is being maintained in the same repository as `emacsql'
-itself. When `libsqlite3', then use the `emacsql-libsqlite3'
-library, which itself uses a module provided by the `sqlite3'
-package. This is still experimental. When `sqlite3', then use the
-`emacsql-sqlite3' library, which uses the official `sqlite3' cli
-tool, which is not recommended because it is not suitable to be
-used like this, but has the advantage that you likely don't need
-a compiler. See https://nullprogram.com/blog/2014/02/06/."
-  :package-version '(org-roam . "2.2.0")
-  :group 'org-roam
+itself.
+If you are using Emacs 29, then the recommended connector is
+`sqlite-builtin', which uses the new builtin support for SQLite.
+You need to install the `emacsql-sqlite-builtin' package to use
+this connector.
+If you are using an older Emacs release, then the recommended
+connector is `sqlite-module', which uses the module provided by
+the `sqlite3' package.  This is very similar to the previous
+connector and the built-in support in Emacs 29 derives from this
+module.  You need to install the `emacsql-sqlite-module' package
+to use this connector.
+For the time being `libsqlite3' is still supported.  Do not use
+this, it is an older version of the `sqlite-module' connector
+from before the connector and the package were renamed.
+For the time being `sqlite3' is also supported.  Do not use this.
+This uses the third-party `emacsql-sqlite3' package, which uses
+the official `sqlite3' cli tool, which is not intended
+to be used like this.  See https://nullprogram.com/blog/2014/02/06/."
+  :package-version '(forge . "0.3.0")
+  :group 'forge
  :type '(choice (const sqlite)
-                 (const libsqlite3)
-                 (const sqlite3)
-                 (symbol :tag "other")))
+                 (const sqlite-builtin)
+                 (const sqlite-module)
+                 (const :tag "libsqlite3 (OBSOLETE)" libsqlite3)
+                 (const :tag "sqlite3 (BROKEN)" sqlite3)))

-(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
+(defcustom org-roam-db-location (locate-user-emacs-file "org-roam.db")
  "The path to file where the Org-roam database is stored.

 It is the user's responsibility to set this correctly, especially
@ -98,15 +110,35 @@ slow."
  :type 'boolean
  :group 'org-roam)

+(defcustom org-roam-db-extra-links-elements '(node-property keyword)
+  "The list of Org element types to include for parsing by Org-roam.
+
+By default, when parsing Org's AST, links within keywords and
+property drawers are not parsed as links. Sometimes however, it
+is desirable to parse and cache these links (e.g. hiding links in
+a property drawer)."
+  :package-version '(org-roam . "2.2.0")
+  :group 'org-roam
+  :type '(set (const :tag "keywords" keyword)
+              (const :tag "property drawers" node-property)))
+
+(defcustom org-roam-db-extra-links-exclude-keys '((node-property . ("ROAM_REFS"))
+                                                  (keyword . ("transclude")))
+  "Keys to ignore when mapping over links.
+
+The car of the association list is the Org element type (e.g.
+keyword). The cdr is a list of case-insensitive strings to
+exclude from being treated as links.
+
+For example, we use this to prevent self-referential links in
+ROAM_REFS."
+  :package-version '(org-roam . "2.2.0")
+  :group 'org-roam
+  :type '(alist))
+
 ;;; Variables
 (defconst org-roam-db-version 18)

-;; TODO Rename this
-(defconst org-roam--sqlite-available-p
-  (with-demoted-errors "Org-roam initialization: %S"
-    (emacsql-sqlite-ensure-binary)
-    t))
-
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
  "Database connection to Org-roam database.")

@ -117,8 +149,10 @@ slow."
           org-roam-db--connection))

 (declare-function emacsql-sqlite "ext:emacsql-sqlite")
-(declare-function emacsql-libsqlite3 "ext:emacsql-libsqlite3")
 (declare-function emacsql-sqlite3 "ext:emacsql-sqlite3")
+(declare-function emacsql-libsqlite3 "ext:emacsql-libsqlite3")
+(declare-function emacsql-sqlite-builtin "ext:emacsql-sqlite-builtin")
+(declare-function emacsql-sqlite-module "ext:emacsql-sqlite-module")

 (defun org-roam-db--conn-fn ()
  "Return the function for creating the database connection."
@ -127,6 +161,14 @@ slow."
     (progn
       (require 'emacsql-sqlite)
       #'emacsql-sqlite))
+    (sqlite-builtin
+     (progn
+       (require 'emacsql-sqlite-builtin)
+       #'emacsql-sqlite-builtin))
+    (sqlite-module
+     (progn
+       (require 'emacsql-sqlite-module)
+       #'emacsql-sqlite-module))
    (libsqlite3
     (progn
       (require 'emacsql-libsqlite3)
@ -145,7 +187,9 @@ Performs a database upgrade when required."
    (let ((init-db (not (file-exists-p org-roam-db-location))))
      (make-directory (file-name-directory org-roam-db-location) t)
      (let ((conn (funcall (org-roam-db--conn-fn) org-roam-db-location)))
-        (when-let ((process (emacsql-process conn)))
+        (emacsql conn [:pragma (= foreign_keys ON)])
+        (when-let* ((process (emacsql-process conn))
+                    (_ (processp process)))
          (set-process-query-on-exit-flag process nil))
        (puthash (expand-file-name (file-name-as-directory org-roam-directory))
                 conn
@ -243,7 +287,6 @@ The query is expected to be able to fail, in this situation, run HANDLER."

 (defun org-roam-db--init (db)
  "Initialize database DB with the correct schema and user version."
-  (emacsql db [:pragma (= foreign_keys ON)])
  (emacsql-with-transaction db
    (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
      (emacsql db [:create-table $i1 $S2] table schema))
@ -359,15 +402,12 @@ If UPDATE-P is non-nil, first remove the file in the database."
         ;; Links correctly recognized by Org Mode
         ((eq type 'link)
          (setq link element))
-         ;; Prevent self-referencing links in ROAM_REFS
-         ((and (eq type 'node-property)
-               (org-roam-string-equal (org-element-property :key element) "ROAM_REFS"))
-          nil)
         ;; Links in property drawers and lines starting with #+. Recall that, as for Org Mode v9.4.4, the
         ;; org-element-type of links within properties drawers is "node-property" and for lines starting with
         ;; #+ is "keyword".
-         ((and (or (eq type 'node-property)
-                   (eq type 'keyword))
+         ((and (member type org-roam-db-extra-links-elements)
+               (not (member-ignore-case (org-element-property :key element)
+                                        (cdr (assoc type org-roam-db-extra-links-exclude-keys))))
               (setq bounds (org-in-regexp org-link-any-re))
               (setq link (buffer-substring-no-properties
                           (car bounds)
@ -482,9 +522,24 @@ INFO is the org-element parsed buffer."
    (let (rows)
      (dolist (ref refs)
        (save-match-data
-          (cond ((string-prefix-p "@" ref)
+          (cond (;; @citeKey
+                 (string-prefix-p "@" ref)
                 (push (vector node-id (substring ref 1) "cite") rows))
-                ((string-match org-link-plain-re ref)
+                (;; [cite:@citeKey]
+                 (string-prefix-p "[cite:" ref)
+                 (condition-case nil
+                     (let ((cite-obj (org-cite-parse-objects ref)))
+                       (org-element-map cite-obj 'citation-reference
+                         (lambda (cite)
+                           (let ((key (org-element-property :key cite)))
+                             (push (vector node-id key "cite") rows)))))
+                   (error
+                    (lwarn '(org-roam) :warning
+                           "%s:%s\tInvalid cite %s, skipping..." (buffer-file-name) (point) ref))))
+                (;; https://google.com, cite:citeKey
+                 ;; Note: we use string-match here because it matches any link: e.g. [[cite:abc][abc]]
+                 ;; But this form of matching is loose, and can accept invalid links e.g. [[cite:abc]
+                 (string-match org-link-plain-re ref)
                 (let ((link-type (match-string 1 ref))
                       (path (match-string 2 ref)))
                   (if (and (boundp 'org-ref-cite-types)
@ -585,27 +640,27 @@ in `org-roam-db-sync'."
        (org-roam-require '(org-ref oc)))
      (org-roam-with-file file-path nil
        (emacsql-with-transaction (org-roam-db)
-          (save-excursion
-            (org-set-regexps-and-options 'tags-only)
-            (org-refresh-category-properties)
-            (org-roam-db-clear-file)
-            (org-roam-db-insert-file)
-            (org-roam-db-insert-file-node)
-            (setq org-outline-path-cache nil)
-            (org-roam-db-map-nodes
-             (list #'org-roam-db-insert-node-data
-                   #'org-roam-db-insert-aliases
-                   #'org-roam-db-insert-tags
-                   #'org-roam-db-insert-refs))
-            (setq org-outline-path-cache nil)
-            (setq info (org-element-parse-buffer))
-            (org-roam-db-map-links
-             (list #'org-roam-db-insert-link))
-            (when (fboundp 'org-cite-insert)
-              (require 'oc)             ;ensure feature is loaded
-              (org-roam-db-map-citations
-               info
-               (list #'org-roam-db-insert-citation)))))))))
+          (org-with-wide-buffer
+           (org-set-regexps-and-options 'tags-only)
+           (org-refresh-category-properties)
+           (org-roam-db-clear-file)
+           (org-roam-db-insert-file)
+           (org-roam-db-insert-file-node)
+           (setq org-outline-path-cache nil)
+           (org-roam-db-map-nodes
+            (list #'org-roam-db-insert-node-data
+                  #'org-roam-db-insert-aliases
+                  #'org-roam-db-insert-tags
+                  #'org-roam-db-insert-refs))
+           (setq org-outline-path-cache nil)
+           (setq info (org-element-parse-buffer))
+           (org-roam-db-map-links
+            (list #'org-roam-db-insert-link))
+           (when (fboundp 'org-cite-insert)
+             (require 'oc)             ;ensure feature is loaded
+             (org-roam-db-map-citations
+              info
+              (list #'org-roam-db-insert-citation)))))))))

 ;;;###autoload
 (defun org-roam-db-sync (&optional force)
--- a/org-roam-id.el
+++ b/org-roam-id.el
@ -0,0 +1,117 @@
+;;; org-roam-id.el --- ID-related utilities for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "3.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This module provides ID-related facilities using the Org-roam database.
+;;
+;;; Code:
+(require 'org-id)
+
+(defun org-roam-id-at-point ()
+  "Return the ID at point, if any.
+Recursively traverses up the headline tree to find the
+first encapsulating ID."
+  (org-with-wide-buffer
+   (org-back-to-heading-or-point-min t)
+   (while (and (not (org-roam-db-node-p))
+               (not (bobp)))
+     (org-roam-up-heading-or-point-min))
+   (when (org-roam-db-node-p)
+     (org-id-get))))
+
+(defun org-roam-id-find (id &optional markerp)
+  "Return the location of the entry with the id ID using the Org-roam db.
+The return value is a cons cell (file-name . position), or nil
+if there is no entry with that ID.
+With optional argument MARKERP, return the position as a new marker."
+  (cond
+   ((symbolp id) (setq id (symbol-name id)))
+   ((numberp id) (setq id (number-to-string id))))
+  (let ((node (org-roam-populate (org-roam-node-create :id id))))
+    (when-let ((file (org-roam-node-file node)))
+      (if markerp
+          (unwind-protect
+              (let ((buffer (or (find-buffer-visiting file)
+                                (find-file-noselect file))))
+                (with-current-buffer buffer
+                  (move-marker (make-marker) (org-roam-node-point node) buffer))))
+        (cons (org-roam-node-file node)
+              (org-roam-node-point node))))))
+
+(defun org-roam-id-open (id _)
+  "Go to the entry with id ID.
+Like `org-id-open', but additionally uses the Org-roam database."
+  (org-mark-ring-push)
+  (let ((m (or (org-roam-id-find id 'marker)
+               (org-id-find id 'marker)))
+        cmd)
+    (unless m
+      (error "Cannot find entry with ID \"%s\"" id))
+    ;; Use a buffer-switching command in analogy to finding files
+    (setq cmd
+          (or
+           (cdr
+            (assq
+             (cdr (assq 'file org-link-frame-setup))
+             '((find-file . switch-to-buffer)
+               (find-file-other-window . switch-to-buffer-other-window)
+               (find-file-other-frame . switch-to-buffer-other-frame))))
+           'switch-to-buffer-other-window))
+    (if (not (equal (current-buffer) (marker-buffer m)))
+        (funcall cmd (marker-buffer m)))
+    (goto-char m)
+    (move-marker m nil)
+    (org-show-context)))
+
+(org-link-set-parameters "id" :follow #'org-roam-id-open)
+
+;;;###autoload
+(defun org-roam-update-org-id-locations (&rest directories)
+  "Scan Org-roam files to update `org-id' related state.
+This is like `org-id-update-id-locations', but will automatically
+use the currently bound `org-directory' and `org-roam-directory'
+along with DIRECTORIES (if any), where the lookup for files in
+these directories will be always recursive.
+
+Note: Org-roam doesn't have hard dependency on
+`org-id-locations-file' to lookup IDs for nodes that are stored
+in the database, but it still tries to properly integrates with
+`org-id'. This allows the user to cross-reference IDs outside of
+the current `org-roam-directory', and also link with \"id:\"
+links to headings/files within the current `org-roam-directory'
+that are excluded from identification in Org-roam as
+`org-roam-node's, e.g. with \"ROAM_EXCLUDE\" property."
+  (interactive)
+  (cl-loop for dir in (cons org-roam-directory directories)
+           for org-roam-directory = dir
+           nconc (org-roam-list-files) into files
+           finally (org-id-update-id-locations files org-roam-verbose)))
+
+(provide 'org-roam-id)
+
+;;; org-roam-id.el ends here
--- a/org-roam-log.el
+++ b/org-roam-log.el
@ -0,0 +1,53 @@
+;;; org-roam-log.el --- Integrations with Org-log -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2022-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This module provides integrations with Org-log.
+;;
+;;; Code:
+(require 'org-roam)
+
+(defcustom org-roam-log-setup-hook nil
+  "Hook run when a log for an Org-roam file is setup."
+  :group 'org-roam
+  :type 'hook)
+
+(defun org-roam-log-p ()
+  "Return t if the log buffer is for an Org-roam file, nil otherwise."
+  (and org-log-note-marker
+       (org-roam-file-p (buffer-file-name (marker-buffer org-log-note-marker)))))
+
+(defun org-roam-log--setup ()
+  "Run hooks in `org-roam-log-setup-hook'."
+  (run-hooks 'org-roam-log-setup-hook))
+
+(add-hook 'org-roam-log-setup-hook #'org-roam--register-completion-functions-h)
+(add-hook 'org-log-buffer-setup-hook #'org-roam-log--setup)
+
+(provide 'org-roam-log)
+;;; org-roam-log.el ends here
--- a/org-roam-migrate.el
+++ b/org-roam-migrate.el
@ -1,12 +1,12 @@
 ;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))

 ;; This file is NOT part of GNU Emacs.

--- a/org-roam-mode.el
+++ b/org-roam-mode.el
@ -1,12 +1,12 @@
 ;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))

 ;; This file is NOT part of GNU Emacs.

@ -39,14 +39,28 @@
 (defvar org-ref-buffer-hacked)

 ;;; Options
-(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
-                                                 #'org-roam-reflinks-section)
-  "Functions that insert sections in the `org-roam-mode' based buffers.
-Each function is called with one argument, which is an
-`org-roam-node' for which the buffer will be constructed for.
-Normally this node is `org-roam-buffer-current-node'."
+(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
+                                        #'org-roam-reflinks-section)
+  "A list of sections for the `org-roam-mode' based buffers.
+Each section is a function that is passed the an `org-roam-node'
+for which the section will be constructed for as the first
+argument. Normally this node is `org-roam-buffer-current-node'.
+The function may also accept other optional arguments. Each item
+in the list is either:
+
+1. A function, which is called only with the `org-roam-node' as the argument
+2. A list, containing the function and the optional arguments.
+
+For example, one can add
+
+    (org-roam-backlinks-section :unique t)
+
+to the list to pass :unique t to the section-rendering function."
  :group 'org-roam
-  :type 'hook)
+  :type `(repeat (choice (symbol :tag "Function")
+                         (list :tag "Function with arguments"
+                               (symbol :tag "Function")
+                               (repeat :tag "Arguments" :inline t (sexp :tag "Arg"))))))

 (defcustom org-roam-buffer-postrender-functions (list)
  "Functions to run after the Org-roam buffer is rendered.
@ -168,7 +182,7 @@ This mode is used by special Org-roam buffers, such as persistent
 `org-roam-buffer' and dedicated Org-roam buffers
 \(`org-roam-buffer-display-dedicated'), which render the
 information in a section-like manner (see
-`org-roam-mode-section-functions'), with which the user can
+`org-roam-mode-sections'), with which the user can
 interact with."
  :group 'org-roam
  (face-remap-add-relative 'header-line 'org-roam-header-line))
@ -228,7 +242,14 @@ buffer."
     (org-roam-node-title org-roam-buffer-current-node))
    (magit-insert-section (org-roam)
      (magit-insert-heading)
-      (run-hook-with-args 'org-roam-mode-section-functions org-roam-buffer-current-node))
+      (dolist (section org-roam-mode-sections)
+        (pcase section
+          ((pred functionp)
+           (funcall section org-roam-buffer-current-node))
+          (`(,fn . ,args)
+           (apply fn (cons org-roam-buffer-current-node args)))
+          (_
+           (user-error "Invalid `org-roam-mode-sections' specification")))))
    (run-hooks 'org-roam-buffer-postrender-functions)
    (goto-char 0)))

@ -289,7 +310,7 @@ To toggle its display use `org-roam-buffer-toggle' command.")
  (pcase (org-roam-buffer--visibility)
    ('visible
     (progn
-       (delete-window (get-buffer-window org-roam-buffer))
+       (quit-window nil (get-buffer-window org-roam-buffer))
       (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
    ((or 'exists 'none)
     (progn
@ -428,10 +449,12 @@ In interactive calls OTHER-WINDOW is set with

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

 (defun org-roam-preview-get-contents (file pt)
@ -459,14 +482,23 @@ headline, up to the next headline."
        (org-roam-populate (org-roam-backlink-target-node backlink)))
  backlink)

-(defun org-roam-backlinks-get (node)
-  "Return the backlinks for NODE."
-  (let ((backlinks (org-roam-db-query
-                    [:select [source dest pos properties]
-                     :from links
-                     :where (= dest $s1)
-                     :and (= type "id")]
-                    (org-roam-node-id node))))
+(cl-defun org-roam-backlinks-get (node &key unique)
+  "Return the backlinks for NODE.
+
+ When UNIQUE is nil, show all positions where references are found.
+ When UNIQUE is t, limit to unique sources."
+  (let* ((sql (if unique
+                  [:select :distinct [source dest pos properties]
+                   :from links
+                   :where (= dest $s1)
+                   :and (= type "id")
+                   :group :by source
+                   :having (funcall min pos)]
+                [:select [source dest pos properties]
+                 :from links
+                 :where (= dest $s1)
+                 :and (= type "id")]))
+         (backlinks (org-roam-db-query sql (org-roam-node-id node))))
    (cl-loop for backlink in backlinks
             collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
                       (org-roam-populate
@ -482,9 +514,12 @@ Sorts by title."
  (string< (org-roam-node-title (org-roam-backlink-source-node a))
           (org-roam-node-title (org-roam-backlink-source-node b))))

-(defun org-roam-backlinks-section (node)
-  "The backlinks section for NODE."
-  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node))))
+(cl-defun org-roam-backlinks-section (node &key (unique nil))
+  "The backlinks section for NODE.
+
+When UNIQUE is nil, show all positions where references are found.
+When UNIQUE is t, limit to unique sources."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node :unique unique))))
    (magit-insert-section (org-roam-backlinks)
      (magit-insert-heading "Backlinks:")
      (dolist (backlink backlinks)
@ -622,7 +657,7 @@ References from FILE are excluded."
                                (shell-command-to-string "rg --pcre2-version"))))
    (let* ((titles (cons (org-roam-node-title node)
                         (org-roam-node-aliases node)))
-           (rg-command (concat "rg -o --vimgrep -P -i "
+           (rg-command (concat "rg -L -o --vimgrep -P -i "
                               (mapconcat (lambda (glob) (concat "-g " glob))
                                          (org-roam--list-files-search-globs org-roam-file-extensions)
                                          " ")
@ -643,7 +678,7 @@ References from FILE are excluded."
                    col (string-to-number (match-string 3 line))
                    match (match-string 4 line))
              (when (and match
-                         (not (f-equal-p (org-roam-node-file node) f))
+                         (not (file-equal-p (org-roam-node-file node) f))
                         (member (downcase match) (mapcar #'downcase titles)))
                (magit-insert-section section (org-roam-grep-section)
                  (oset section file f)
--- a/org-roam-node.el
+++ b/org-roam-node.el
@ -1,11 +1,11 @@
 ;;; org-roam-node.el --- Interfacing and interacting with nodes -*- lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
+;; Version: 2.2.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "3.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -36,8 +36,7 @@

 ;;; Options
 ;;;; Completing-read
-(defcustom org-roam-node-display-template
-  (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag))
+(defcustom org-roam-node-display-template "${title}"
  "Configures display formatting for Org-roam node.
 Patterns of form \"${field-name:length}\" are interpolated based
 on the current node.
@ -132,7 +131,8 @@ It takes a single argument REF, which is a propertized string."
  :type 'boolean)

 (defcustom org-roam-extract-new-file-path "%<%Y%m%d%H%M%S>-${slug}.org"
-  "The file path to use when a node is extracted to its own file."
+  "The file path template to use when a node is extracted to its own file.
+This path is relative to `org-roam-directory'."
  :group 'org-roam
  :type 'string)

@ -175,6 +175,7 @@ It takes a single argument REF, which is a propertized string."
                           776 ; U+0308 COMBINING DIAERESIS
                           777 ; U+0309 COMBINING HOOK ABOVE
                           778 ; U+030A COMBINING RING ABOVE
+                           779 ; U+030B COMBINING DOUBLE ACUTE ACCENT
                           780 ; U+030C COMBINING CARON
                           795 ; U+031B COMBINING HORN
                           803 ; U+0323 COMBINING DOT BELOW
@ -186,14 +187,12 @@ It takes a single argument REF, which is a propertized string."
                           816 ; U+0330 COMBINING TILDE BELOW
                           817 ; U+0331 COMBINING MACRON BELOW
                           )))
-    (cl-flet* ((nonspacing-mark-p (char)
-                                  (memq char slug-trim-chars))
-               (strip-nonspacing-marks (s)
-                                       (string-glyph-compose
-                                        (apply #'string (seq-remove #'nonspacing-mark-p
-                                                                    (string-glyph-decompose s)))))
-               (cl-replace (title pair)
-                           (replace-regexp-in-string (car pair) (cdr pair) title)))
+    (cl-flet* ((nonspacing-mark-p (char) (memq char slug-trim-chars))
+               (strip-nonspacing-marks (s) (string-glyph-compose
+                                            (apply #'string
+                                                   (seq-remove #'nonspacing-mark-p
+                                                               (string-glyph-decompose s)))))
+               (cl-replace (title pair) (replace-regexp-in-string (car pair) (cdr pair) title)))
      (let* ((pairs `(("[^[:alnum:][:digit:]]" . "_") ;; convert anything not alphanumeric
                      ("__*" . "_")                   ;; remove sequential underscores
                      ("^_" . "")                     ;; remove starting underscore
@ -426,19 +425,41 @@ GROUP BY id")))
                              all-titles)))))

 ;;;; Finders
-(defun org-roam-node-find-noselect (node &optional force)
-  "Navigate to the point for NODE, and return the buffer.
-If NODE is already visited, this won't automatically move the
-point to the beginning of the NODE, unless FORCE is non-nil."
-  (unless (org-roam-node-file node)
-    (user-error "Node does not have corresponding file"))
-  (let ((buf (find-file-noselect (org-roam-node-file node))))
-    (with-current-buffer buf
-      (when (or force
-                (not (equal (org-roam-node-id node)
-                            (org-roam-id-at-point))))
-        (goto-char (org-roam-node-point node))))
-    buf))
+(defun org-roam-node-marker (node)
+  "Get the marker for NODE."
+  (unwind-protect
+      (let* ((file (org-roam-node-file node))
+             (buffer (or (find-buffer-visiting file)
+                         (find-file-noselect file))))
+        (with-current-buffer buffer
+          (move-marker (make-marker) (org-roam-node-point node) buffer)))))
+
+(defun org-roam-node-open (node &optional cmd force)
+  "Go to the node NODE.
+CMD is the command used to display the buffer. If not provided,
+`org-link-frame-setup' is respected. Assumes that the node is
+fully populated, with file and point. If NODE is already visited,
+this won't automatically move the point to the beginning of the
+NODE, unless FORCE is non-nil."
+  (interactive (list (org-roam-node-at-point) current-prefix-arg))
+  (org-mark-ring-push)
+  (let ((m (org-roam-node-marker node))
+        (cmd (or cmd
+                 (cdr
+                  (assq
+                   (cdr (assq 'file org-link-frame-setup))
+                   '((find-file . switch-to-buffer)
+                     (find-file-other-window . switch-to-buffer-other-window)
+                     (find-file-other-frame . switch-to-buffer-other-frame))))
+                 'switch-to-buffer-other-window)))
+    (if (not (equal (current-buffer) (marker-buffer m)))
+        (funcall cmd (marker-buffer m)))
+    (when (or force
+              (not (equal (org-roam-node-id node)
+                          (org-roam-id-at-point))))
+      (goto-char m))
+    (move-marker m nil))
+  (org-show-context))

 (defun org-roam-node-visit (node &optional other-window force)
  "From the current buffer, visit NODE. Return the visited buffer.
@ -450,13 +471,10 @@ If NODE is already visited, this won't automatically move the
 point to the beginning of the NODE, unless FORCE is non-nil. In
 interactive calls FORCE always set to t."
  (interactive (list (org-roam-node-at-point t) current-prefix-arg t))
-  (let ((buf (org-roam-node-find-noselect node force))
-        (display-buffer-fn (if other-window
+  (org-roam-node-open node (if other-window
                               #'switch-to-buffer-other-window
-                             #'pop-to-buffer-same-window)))
-    (funcall display-buffer-fn buf)
-    (when (org-invisible-p) (org-show-context))
-    buf))
+                             #'pop-to-buffer-same-window)
+                      force))

 ;;;###autoload
 (cl-defun org-roam-node-find (&optional other-window initial-input filter-fn &key templates)
@ -477,16 +495,16 @@ The TEMPLATES, if provided, override the list of capture templates (see
       :props '(:finalize find-file)))))

 ;;;###autoload
-(defun org-roam-node-random (&optional other-window)
+(defun org-roam-node-random (&optional other-window filter-fn)
  "Find and open a random Org-roam node.
 With prefix argument OTHER-WINDOW, visit the node in another
-window instead."
+window instead.
+FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
+and when nil is returned the node will be filtered out."
  (interactive current-prefix-arg)
-  (let ((random-row (seq-random-elt (org-roam-db-query [:select [id file pos] :from nodes]))))
-    (org-roam-node-visit (org-roam-node-create :id (nth 0 random-row)
-                                               :file (nth 1 random-row)
-                                               :point (nth 2 random-row))
-                         other-window)))
+  (org-roam-node-visit
+   (cdr (seq-random-elt (org-roam-node-read--completions filter-fn)))
+   other-window))

 ;;;; Completing-read interface
 (defun org-roam-node-read (&optional initial-input filter-fn sort-fn require-match prompt)
@ -498,17 +516,7 @@ SORT-FN is a function to sort nodes. See `org-roam-node-read-sort-by-file-mtime'
 for an example sort function.
 If REQUIRE-MATCH, the minibuffer prompt will require a match.
 PROMPT is a string to show at the beginning of the mini-buffer, defaulting to \"Node: \""
-  (let* ((nodes (org-roam-node-read--completions))
-         (nodes (if filter-fn
-                    (cl-remove-if-not
-                     (lambda (n) (funcall filter-fn (cdr n)))
-                     nodes)
-                  nodes))
-         (sort-fn (or sort-fn
-                      (when org-roam-node-default-sort
-                        (intern (concat "org-roam-node-read-sort-by-"
-                                        (symbol-name org-roam-node-default-sort))))))
-         (_ (when sort-fn (setq nodes (seq-sort sort-fn nodes))))
+  (let* ((nodes (org-roam-node-read--completions filter-fn sort-fn))
         (prompt (or prompt "Node: "))
         (node (completing-read
                prompt
@ -529,15 +537,31 @@ PROMPT is a string to show at the beginning of the mini-buffer, defaulting to \"
    (or (cdr (assoc node nodes))
        (org-roam-node-create :title node))))

-(defun org-roam-node-read--completions ()
+(defun org-roam-node-read--completions (&optional filter-fn sort-fn)
  "Return an alist for node completion.
 The car is the displayed title or alias for the node, and the cdr
 is the `org-roam-node'.
+FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
+and when nil is returned the node will be filtered out.
+SORT-FN is a function to sort nodes. See `org-roam-node-read-sort-by-file-mtime'
+for an example sort function.
 The displayed title is formatted according to `org-roam-node-display-template'."
-  (let ((template (org-roam-node--process-display-format org-roam-node-display-template))
-        (nodes (org-roam-node-list)))
-    (mapcar (lambda (node)
-              (org-roam-node-read--to-candidate node template)) nodes)))
+  (let* ((template (org-roam-node--process-display-format org-roam-node-display-template))
+         (nodes (org-roam-node-list))
+         (nodes (mapcar (lambda (node)
+                          (org-roam-node-read--to-candidate node template)) nodes))
+         (nodes (if filter-fn
+                    (cl-remove-if-not
+                     (lambda (n) (funcall filter-fn (cdr n)))
+                     nodes)
+                  nodes))
+         (sort-fn (or sort-fn
+                      (when org-roam-node-default-sort
+                        (intern (concat "org-roam-node-read-sort-by-"
+                                        (symbol-name org-roam-node-default-sort))))))
+         (nodes (if sort-fn (seq-sort sort-fn nodes)
+                  nodes)))
+    nodes))

 (defun org-roam-node-read--to-candidate (node template)
  "Return a minibuffer completion candidate given NODE.
@ -545,7 +569,8 @@ TEMPLATE is the processed template used to format the entry."
  (let ((candidate-main (org-roam-node--format-entry
                         template
                         node
-                         (1- (frame-width)))))
+                         (1- (if (bufferp (current-buffer))
+                                 (window-width) (frame-width))))))
    (cons (propertize candidate-main 'node node) node)))

 (defun org-roam-node--format-entry (template node &optional width)
@ -663,9 +688,13 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
                  (delete-region beg end)
                  (set-marker beg nil)
                  (set-marker end nil))
-                (insert (org-link-make-string
-                         (concat "id:" (org-roam-node-id node))
-                         description)))
+                (let ((id (org-roam-node-id node)))
+                  (insert (org-link-make-string
+                           (concat "id:" id)
+                           description))
+                  (run-hook-with-args 'org-roam-post-node-insert-hook
+                                      id
+                                      description)))
            (org-roam-capture-
             :node node
             :info info
@ -673,31 +702,10 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
             :props (append
                     (when (and beg end)
                       (list :region (cons beg end)))
-                     (list :insert-at (point-marker)
-                           :link-description description
+                     (list :link-description description
                           :finalize 'insert-link))))))
    (deactivate-mark)))

-(add-hook 'org-roam-find-file-hook #'org-roam-open-id-with-org-roam-db-h)
-(defun org-roam-open-id-with-org-roam-db-h ()
-  "Try to open \"id:\" links at point by querying them to the database."
-  (add-hook 'org-open-at-point-functions #'org-roam-open-id-at-point nil t))
-
-(defun org-roam-open-id-at-point ()
-  "Navigate to \"id:\" link at point using the Org-roam database."
-  (when (org-in-regexp org-link-any-re)
-    (let ((link (match-string 2))
-          id)
-      (when (string-prefix-p "id:" link)
-        (setq id (substring-no-properties link 3))
-        (let ((node (org-roam-populate (org-roam-node-create :id id))))
-          (cond
-           ((org-roam-node-file node)
-            (org-mark-ring-push)
-            (org-roam-node-visit node nil 'force)
-            t)
-           (t nil)))))))
-
 ;;;;; [roam:] link
 (org-link-set-parameters "roam" :follow #'org-roam-link-follow-link)
 (defun org-roam-link-follow-link (title-or-alias)
@ -794,6 +802,8 @@ hence \"everywhere\"."
            :exclusive 'no))))

 (add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions-h)
+(add-hook 'org-roam-indirect-buffer-hook #'org-roam--register-completion-functions-h)
+
 (defun org-roam--register-completion-functions-h ()
  "Setup `org-roam-completion-functions' for `completion-at-point'."
  (dolist (f org-roam-completion-functions)
@ -811,7 +821,8 @@ Any tags declared on #+FILETAGS: are transferred to tags on the new top heading.
 Any top level properties drawers are incorporated into the new heading."
  (interactive)
  (org-with-point-at 1
-    (org-map-entries 'org-do-demote)
+    (org-map-region #'org-do-demote
+                    (point-min) (point-max))
    (insert "* "
            (org-roam--get-keyword "title")
            "\n")
@ -820,21 +831,40 @@ Any top level properties drawers are incorporated into the new heading."
    (org-roam-erase-keyword "title")
    (org-roam-erase-keyword "filetags")))

+(defun org-roam--h1-count ()
+  "Count level-1 headings in the current file."
+  (let ((h1-count 0))
+    (org-with-wide-buffer
+     (org-map-region (lambda ()
+                       (if (= (org-current-level) 1)
+                           (incf h1-count)))
+                     (point-min) (point-max))
+     h1-count)))
+
+(defun org-roam--buffer-promoteable-p ()
+  "Verify that this buffer is promoteable:
+There is a single level-1 heading
+and no extra content before the first heading."
+  (and
+   (= (org-roam--h1-count) 1)
+   (org-with-point-at 1 (org-at-heading-p))))
+
 (defun org-roam-promote-entire-buffer ()
  "Promote the current buffer.
-Converts a file containing a headline node at the top to a file
+Converts a file containing a single level-1 headline node to a file
 node."
  (interactive)
+  (unless (org-roam--buffer-promoteable-p)
+    (user-error "Cannot promote: multiple root headings or there is extra file-level text"))
  (org-with-point-at 1
-    (org-map-entries (lambda ()
-                       (when (> (org-outline-level) 1)
-                         (org-do-promote))))
    (let ((title (nth 4 (org-heading-components)))
-          (tags (nth 5 (org-heading-components))))
-      (beginning-of-line)
-      (kill-line 1)
-      (org-roam-set-keyword "title" title)
-      (when tags (org-roam-set-keyword "filetags" tags)))))
+          (tags (org-get-tags)))
+      (kill-whole-line)
+      (org-roam-end-of-meta-data)
+      (insert "#+title: " title "\n")
+      (when tags (org-roam-tag-add tags))
+      (org-map-region #'org-promote (point-min) (point-max))
+      (org-roam-db-update-file))))

 ;;;###autoload
 (defun org-roam-refile ()
@ -920,53 +950,21 @@ If region is active, then use it instead of the node at point."
                           (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
                                (plist-put template-info ksym r)
                                r)))))))
-           (file-path (read-file-name "Extract node to: "
-                                      (file-name-as-directory org-roam-directory) template nil template)))
+           (file-path
+            (expand-file-name
+             (read-file-name "Extract node to: "
+                             (file-name-as-directory org-roam-directory) template nil template)
+             org-roam-directory)))
      (when (file-exists-p file-path)
        (user-error "%s exists. Aborting" file-path))
      (org-cut-subtree)
      (save-buffer)
      (with-current-buffer (find-file-noselect file-path)
        (org-paste-subtree)
+        (while (> (org-current-level) 1) (org-promote-subtree))
        (org-roam-promote-entire-buffer)
        (save-buffer)))))

-;;; IDs
-;;;; Getters
-(defun org-roam-id-at-point ()
-  "Return the ID at point, if any.
-Recursively traverses up the headline tree to find the
-first encapsulating ID."
-  (org-with-wide-buffer
-   (org-back-to-heading-or-point-min t)
-   (while (and (not (org-roam-db-node-p))
-               (not (bobp)))
-     (org-roam-up-heading-or-point-min))
-   (when (org-roam-db-node-p)
-     (org-id-get))))
-
-;;;###autoload
-(defun org-roam-update-org-id-locations (&rest directories)
-  "Scan Org-roam files to update `org-id' related state.
-This is like `org-id-update-id-locations', but will automatically
-use the currently bound `org-directory' and `org-roam-directory'
-along with DIRECTORIES (if any), where the lookup for files in
-these directories will be always recursive.
-
-Note: Org-roam doesn't have hard dependency on
-`org-id-locations-file' to lookup IDs for nodes that are stored
-in the database, but it still tries to properly integrates with
-`org-id'. This allows the user to cross-reference IDs outside of
-the current `org-roam-directory', and also link with \"id:\"
-links to headings/files within the current `org-roam-directory'
-that are excluded from identification in Org-roam as
-`org-roam-node's, e.g. with \"ROAM_EXCLUDE\" property."
-  (interactive)
-  (cl-loop for dir in (cons org-roam-directory directories)
-           for org-roam-directory = dir
-           nconc (org-roam-list-files) into files
-           finally (org-id-update-id-locations files org-roam-verbose)))
-
 ;;; Refs
 ;;;; Completing-read interface
 (defun org-roam-ref-read (&optional initial-input filter-fn)
--- a/org-roam-utils.el
+++ b/org-roam-utils.el
@ -1,11 +1,11 @@
 ;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
+;; Version: 2.2.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4"))

 ;; This file is NOT part of GNU Emacs.
@ -52,6 +52,16 @@
       (org-roam-replace-string "\\" "\\\\")
       (org-roam-replace-string "\"" "\\\"")))

+(defun org-roam-word-wrap (len s)
+  "If S is longer than LEN, wrap the words with newlines."
+  (declare (side-effect-free t))
+  (save-match-data
+    (with-temp-buffer
+      (insert s)
+      (let ((fill-column len))
+        (fill-region (point-min) (point-max)))
+      (buffer-substring (point-min) (point-max)))))
+
 (defun org-roam-string-equal (s1 s2)
  "Return t if S1 and S2 are equal.
 Like `string-equal', but case-insensitive."
@ -59,6 +69,15 @@ Like `string-equal', but case-insensitive."
       (or (string-equal s1 s2)
           (string-equal (downcase s1) (downcase s2)))))

+(defun org-roam-whitespace-content (s)
+  "Return the whitespace content at the end of S."
+  (with-temp-buffer
+    (let ((c 0))
+      (insert s)
+      (skip-chars-backward " \t\n")
+      (buffer-substring-no-properties
+       (point) (point-max)))))
+
 (defun org-roam-strip-comments (s)
  "Strip Org comments from string S."
  (with-temp-buffer
@ -99,6 +118,12 @@ SPEC is a list, as per `dolist'."
    `(dolist ,spec ,@body)))

 ;;; File utilities
+(defun org-roam-descendant-of-p (a b)
+  "Return t if A is descendant of B."
+  (unless (equal (file-truename a) (file-truename b))
+    (string-prefix-p (replace-regexp-in-string "^\\([A-Za-z]\\):" 'downcase (expand-file-name b) t t)
+                     (replace-regexp-in-string "^\\([A-Za-z]\\):" 'downcase (expand-file-name a) t t))))
+
 (defmacro org-roam-with-file (file keep-buf-p &rest body)
  "Execute BODY within FILE.
 If FILE is nil, execute BODY in the current buffer.
@ -119,7 +144,8 @@ Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
         (delay-mode-hooks
           (let ((org-inhibit-startup t)
                 (org-agenda-files nil))
-             (org-mode))))
+             (org-mode)
+             (hack-local-variables))))
       (setq res (progn ,@body))
       (unless (and new-buf (not ,keep-buf-p))
         (save-buffer)))
@ -460,7 +486,8 @@ See <https://github.com/raxod502/straight.el/issues/520>."
                                         '("Doom" "Spacemacs" "N/A" "I don't know"))
                      (quit "N/A"))))
    (insert (format "- Org: %s\n" (org-version nil 'full)))
-    (insert (format "- Org-roam: %s" (org-roam-version)))))
+    (insert (format "- Org-roam: %s" (org-roam-version)))
+    (insert (format "- sqlite-connector: %s" org-roam-database-connector))))


 (provide 'org-roam-utils)
--- a/org-roam.el
+++ b/org-roam.el
@ -1,12 +1,12 @@
 ;;; org-roam.el --- A database abstraction layer for Org-mode -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))

 ;; This file is NOT part of GNU Emacs.

@ -71,7 +71,6 @@
 ;; majority of them can be found at https://github.com/org-roam and MELPA.
 ;;
 ;;; Code:
-(require 'f)
 (require 'dash)

 (require 'rx)
@ -84,6 +83,7 @@
 (require 'emacsql-sqlite)

 (require 'org)
+(require 'org-attach)                   ; To set `org-attach-id-dir'
 (require 'org-id)
 (require 'ol)
 (require 'org-element)
@ -123,6 +123,12 @@ All Org files, at any level of nesting, are considered part of the Org-roam."
  :group 'org-roam
  :type 'hook)

+(defcustom org-roam-post-node-insert-hook nil
+  "Hook run when an Org-roam node is inserted as an Org link.
+Each function takes two arguments: the id of the node, and the link description."
+  :group 'org-roam
+  :type 'hook)
+
 (defcustom org-roam-file-extensions '("org")
  "List of file extensions to be included by Org-Roam.
 While a file extension different from \".org\" may be used, the
@ -131,9 +137,11 @@ responsibility to ensure that."
  :type '(repeat string)
  :group 'org-roam)

-(defcustom org-roam-file-exclude-regexp nil
+(defcustom org-roam-file-exclude-regexp (list org-attach-id-dir)
  "Files matching this regular expression are excluded from the Org-roam."
  :type '(choice
+          (repeat
+           (string :tag "Regular expression matching files to ignore"))
          (string :tag "Regular expression matching files to ignore")
          (const :tag "Include everything" nil))
  :group 'org-roam)
@ -188,14 +196,25 @@ FILE is an Org-roam file if:
         (ext (when path (org-roam--file-name-extension path)))
         (ext (if (string= ext "gpg")
                  (org-roam--file-name-extension (file-name-sans-extension path))
-                ext)))
+                ext))
+         (org-roam-dir-p (org-roam-descendant-of-p path org-roam-directory))
+         (valid-file-ext-p (member ext org-roam-file-extensions))
+         (match-exclude-regexp-p
+          (cond
+           ((not org-roam-file-exclude-regexp) nil)
+           ((stringp org-roam-file-exclude-regexp)
+            (string-match-p org-roam-file-exclude-regexp path))
+           ((listp org-roam-file-exclude-regexp)
+            (let (is-match)
+              (dolist (exclude-re org-roam-file-exclude-regexp)
+                (setq is-match (or is-match (string-match-p exclude-re path))))
+              is-match)))))
    (save-match-data
      (and
       path
-       (member ext org-roam-file-extensions)
-       (not (and org-roam-file-exclude-regexp
-                 (string-match-p org-roam-file-exclude-regexp path)))
-       (f-descendant-of-p path (expand-file-name org-roam-directory))))))
+       org-roam-dir-p
+       valid-file-ext-p
+       (not match-exclude-regexp-p)))))

 (defun org-roam-list-files ()
  "Return a list of all Org-roam files under `org-roam-directory'.
@ -260,7 +279,8 @@ If no files are found, an empty list is returned."
       (shell-command-to-string it)
       (ansi-color-filter-apply it)
       (split-string it "\n")
-       (seq-filter #'s-present? it)))
+       (seq-filter (lambda (s)
+                     (not (or (null s) (string= "" s)))) it)))

 (defun org-roam--list-files-search-globs (exts)
  "Given EXTS, return a list of search globs.
@ -279,8 +299,8 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
 (defun org-roam--list-files-fd (executable dir)
  "Return all Org-roam files under DIR, using \"fd\", provided as EXECUTABLE."
  (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
-         (extensions (string-join (mapcar (lambda (glob) (substring glob 2 -1)) globs) " -e "))
-         (command (string-join `(,executable "-L" ,dir "--type file" ,extensions) " ")))
+         (extensions (string-join (mapcar (lambda (glob) (concat "-e " (substring glob 2 -1))) globs) " "))
+         (command (string-join `(,executable "-L" "--type file" ,extensions "." ,dir) " ")))
    (org-roam--shell-command-files command)))

 (defalias 'org-roam--list-files-fdfind #'org-roam--list-files-fd)
@ -313,8 +333,10 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
  (require 'org-roam-utils)
  (require 'org-roam-db)
  (require 'org-roam-node)
+  (require 'org-roam-id)
  (require 'org-roam-capture)
  (require 'org-roam-mode)
+  (require 'org-roam-log)
  (require 'org-roam-migrate))

 ;;; org-roam.el ends here
--- a/tests/test-org-roam-capture.el
+++ b/tests/test-org-roam-capture.el
@ -0,0 +1,56 @@
+;;; test-org-roam-capture.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; 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 <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(describe "org-roam-capture--fill-template"
+  (it "fills template without newline"
+    (expect
+     (org-roam-capture--fill-template "foo")
+     :to-equal "foo"))
+
+  (it "fills template ensuring newline"
+    (expect
+     (org-roam-capture--fill-template "foo" 'ensure-newline)
+     :to-equal "foo\n"))
+
+  (it "fills template with newline"
+    (expect
+     (org-roam-capture--fill-template "foo\n")
+     :to-equal "foo\n"))
+
+  (it "fills template with two newlines"
+    (expect
+     (org-roam-capture--fill-template "foo\n\n")
+     :to-equal "foo\n\n")
+    (expect
+     (org-roam-capture--fill-template "foo\n\t\n")
+     :to-equal "foo\n\t\n"))
+
+  (it "expands templates when it's a function"
+    (expect
+     (org-roam-capture--fill-template (lambda () "foo"))
+     :to-equal "foo")))
+
+(provide 'test-org-roam-capture)
--- a/tests/test-org-roam-utils.el
+++ b/tests/test-org-roam-utils.el
@ -0,0 +1,39 @@
+;;; test-org-roam-utils.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; 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 <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(describe "org-roam-whitespace-content"
+  (it "extracts whitespace correctly"
+    (expect
+     (org-roam-whitespace-content "foo")
+     :to-equal "")
+    (expect
+     (org-roam-whitespace-content "foo\n")
+     :to-equal "\n")
+    (expect
+     (org-roam-whitespace-content "foo\n\t\n")
+     :to-equal "\n\t\n")))
+
+(provide 'test-org-roam-utils)
Author	SHA1	Message	Date
Jethro Kuan	69116a4da4	v2.2.2 (#2171 )	2022-04-24 17:05:27 -07:00
Jethro Kuan	3014c63d50	(feat)log: init (#2170 ) Create initial log module for working with Org logs	2022-04-24 16:57:13 -07:00
c1-g	a073bcff5c	(fix) `org-roam-file-p` handle opening a buffer with no path (#2169 ) * (fix) org-roam-file-p handle opening a buffer with no path Found this issue when opening a .epub file with nov.el (a package that renders EPUB file) because nov.el doesn't store the filename in buffer-file-name, opening it caused errors with org-roam-file-p. * (minor): org-roam-file-p check if filename is non-nil first	2022-04-23 16:36:09 -07:00
Jethro Kuan	b948cfbe37	(github): remove commit from issue template	2022-04-16 20:34:49 -07:00
Jethro Kuan	3716817618	(utils): add sqlite-connector to diagnostics output (#2162 )	2022-04-16 20:32:57 -07:00
Jethro Kuan	608feed855	Update FUNDING.yml	2022-04-16 20:27:34 -07:00
Jethro Kuan	6132155393	(db)fix: fix sqlite-builtin and sqlite-module (#2161 )	2022-04-16 20:26:25 -07:00
Jason May	d8985aa245	(node)refile: fixed org-roam-promote-entire-buffer structure errors (#2091 )	2022-04-16 17:09:50 -07:00
Jethro Kuan	61a544cebd	(core): ignore org-attach-id-dir by default (#2160 )	2022-04-16 14:49:03 -07:00
Jethro Kuan	ddaf7ec10e	(db): fix db sync for narrowed buffers (#2159 ) * (db): fix db sync for narrowed buffers * update changelog	2022-04-16 14:25:41 -07:00
Jethro Kuan	8318da895d	(db): support emacsql-sqlite-{builtin,module} (#2158 ) * (db): support emacsql-sqlite-{builtin,module} Add support for emacsql-sqlite-builtin and emacs-sqlite-module. Fixes #2146. * update changelog	2022-04-16 14:16:39 -07:00
Ahmed Shariff	9eaf91b801	(fix)capture: Process fn capture templates before whitespace-content (#2157 ) * [Fix #2156] Expand fn templates in fill-template before whitespace-content * Update change log and adding tests related to #2157	2022-04-14 09:50:47 -07:00
Ahmed Shariff	3bb45afccb	[Fix #2151 ] org-roam-preview-default-function doesn't copy next node (#2152 )	2022-04-09 16:17:53 -07:00
Jethro Kuan	fee008cdfb	(docs): fix docs build (#2150 ) debian packaging cannot use id links to build docs	2022-04-09 00:54:02 -07:00
Jethro Kuan	36152590ad	(feat)export: init (#2138 )	2022-03-27 11:11:05 -07:00
Jethro Kuan	a69968fc12	(chore): add changelog entry (#2136 )	2022-03-27 10:42:23 -07:00
Ron Parker	d71675fb47	(fix) unlinked-references: search symlinked directories (#2130 ) Use the ripgrep '-L' option to follow directory symlinks. This matches the behavior of `org-roam--list-files-rg'.	2022-03-19 12:02:03 -07:00
Jethro Kuan	3782e88d50	(release): v2.2.1 (#2126 )	2022-03-14 23:37:29 -07:00
lafirest	b4f14eebae	(feat)capture: add org-roam-post-node-insert-hook (#2125 ) * (feat): add org-roam-post-node-insert-hook Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2022-03-14 23:24:55 -07:00
Jethro Kuan	cce6a05630	(fix)buffer: update defcustom for org-roam-mode-section-functions (#2124 )	2022-03-13 09:04:55 -07:00
Jethro Kuan	cc3689f30f	(feat)buffer: pass args to org-mode-section-functions (#2123 ) * (feat)buffer: pass args to org-mode-section-functions * update docs	2022-03-12 21:24:11 -08:00
Jeremy Friesen	b179a5a1a6	(feat)buffer: add unique option for org-roam-backlinks-section (#2121 ) Prior to this commit, when we would render backlinks in the `org-buffer`, we would render each reference. This meant that if a source file referenced the node 5 times, there would be 5 backlink references in the `org-buffer` (one for each position of the reference). With this change, we add a parameter that specifies that backlink sources should be unique. In the above example, that would mean instead of 5 backlinks we'd see 1. And, as a concession, we'd use the lowest position (e.g. the first reference in the source). Closes #2119	2022-03-12 13:12:03 -08:00
Jethro Kuan	9172001c11	(chore)readme: update link (#2120 )	2022-03-11 21:49:24 -08:00
Ron Parker	c51cadfe25	(fix)core: fix broken shell-based file listing methods (#2118 ) Change #2025 broke the `org-roam--shell-command-files` filter that affects all of the `org-roam-list-files-command` methods except `elisp`. This causes `org-roam--list-files` to iterate through the variants executing their commands via `org-roam--shell-command-files` but to not see any output, until it finally lands upon `elisp` and gets some results. The issue is that "#'s-present?" was replaced by (or (null s) (string= "" s)) effectively negating the test and converting it to "#'s-blank?". This addresses that by negating the current test.	2022-03-10 16:07:39 -08:00
Jethro Kuan	f6950a9820	(fix)capture: fill-template preserve whitespace content (#2117 ) * (fix)capture: fill-template preserve whitespace content Preserve the whitespace content given in the capture template, by caching it and then appending it to the output template. For Org-capture's purposes, we need to separately ensure that a newline is present. Adds tests to the various helper functions to illustrate changes. Addresses #2115	2022-03-10 09:46:53 -08:00
Jethro Kuan	feb9179c9f	(docs): add docs for org-protocol (#2116 )	2022-03-09 22:11:05 -08:00
PRESFIL	f50d6e7376	(fix): caching symlinked files (#2112 ) * Revert "(fix): `org-roam-descendant-of-p` bug on Windows (#2089)" This reverts commit `97a342fd3f`. Reason: It seems that the `file-in-directory-p` function proposed in #2089 is provided only for physical directories, does not work as we would like with symlinked directories. It dereferences all the symlinks in its path, and previously seemed related paths cease to be such. Because of this, such notes are ignored and not indexed, although they were indexed earlier.	2022-03-03 22:47:24 -08:00
Jethro Kuan	65ea325071	(fix): place cursor after inserted link for new nodes (#2109 ) Special care is taken not to move the point if the original point is no longer the same (i.e. the user moves the cursor after calling the capture, but before finalizing it). Fixes #2108.	2022-02-27 12:50:45 -08:00
Jethro Kuan	62d311de22	(chore): org-map-entries -> org-map-region (#2107 ) org-map-entries is affected by agenda, while org-map-region is not	2022-02-26 18:07:45 -08:00
lennonhill	c8a360afdd	(fix)capture: don't update org-id-locations if file is unknown (#2103 )	2022-02-24 09:11:20 -08:00
Jethro Kuan	cebe77135a	(fix)capture: always ask before deleting capture (#2100 )	2022-02-20 16:51:41 -08:00
Jethro Kuan	25d828c32e	(chore): fix lints on master (#2099 )	2022-02-20 13:14:58 -08:00
Jethro Kuan	fd97c80a26	(chore): pin eldev install to 10.3 (#2098 )	2022-02-20 10:40:54 -08:00
bing	97a342fd3f	(fix): `org-roam-descendant-of-p` bug on Windows (#2089 ) On Windows, `file-truename` and `directory-file-name` downcase driver label: "C:/" => "c:/", while `expand-file-name` keep the case unchanged. If `org-roam-directory` use upper case driver label, `org-roam-descendant-of-p` will alway return `nil`. Fix by only using `file-truename` in the function.	2022-02-20 10:05:12 -08:00
Ingo Lohmar	d20480bb8d	(fix)node: properly expand extraction file path (#2097 ) Previously, the file-path of the new node in `org-roam-extract-subtree' was incorrect in many circumstances. Expanding w.r.t. the initial prompt directory (ie, `org-roam-directory') fixes that	2022-02-19 19:12:53 -08:00
Noboru Ota	b163c900b8	(fix)capture: correctly update org-id-locations-file after capture (#2086 )	2022-02-08 09:12:42 -08:00
Jethro Kuan	0432b00485	(fix)buffer: buffer-toggle: don't destroy window if `org-roam-node-toggle` reuses window (#2082 ) * (fix)buffer: buffer-toggle: don't destroy buffer if reused Closes #2077 * add changelog	2022-02-06 14:20:24 -08:00
Jeremy Friesen	ccfa97ec3a	(feat): ensuring that :ref info capture in all cases (#2079 ) Let's assume we're evaluating the following region: ```elisp (org-roam-capture- :node (org-roam-node-create :title "Org Roam Homepage") :info '(:ref "https://orgroam.com") :props '(:immediate-finish nil)) ``` Prior to this commit, if you did not require "org-roam-protocol" then `org-roam-capture-` would ignore the `:info '(:ref "https://orgroam.com")` parameter. Once you required "org-roam-protocol" then the callback hooks that process `:info`'s `:ref` will fire regardless of whether it comes from org-roam-protocol. After this commit, you no longer need to require "org-roam-protocol" to ensure that you capture an `:info`'s `:ref`. Why is this useful? When I'm reading through my elfeed RSS feed, I want to capture an article. I could use the org-roam-protocol to do this, but that seems a bit unnecessary given that I'm already in Emacs. Closes org-roam/org-roam#2078	2022-02-06 11:17:16 -08:00
Jürgen Hötzel	86e102d990	(fix)dailies: prevent multiple "dailies/" subdir expansions (#2080 ) (#2080 ) When dynamic binding `org-roam-directory` to the "dailies/" subdirectory also bind `org-roam-dailies-directory` to "./" to prevent invalid expansions in user-defined hook functions. Fixes #2070	2022-02-06 11:16:33 -08:00
Jethro Kuan	eed1df90f5	(feat)id: add org-roam-id module (#2072 )	2022-01-30 22:54:28 -08:00
Jethro Kuan	905564a7eb	(docs)db: document "selecting deleted buffer" error (#2071 )	2022-01-30 11:11:09 -08:00
Michael Eliachevitch	9f7a4a0b02	(feat): allow specifying template keys in remaining org-roam-dailies capture/goto commands (#2065 ) This is an extension of PR #2028 [1] by @astery, where the `keys` argument was added to `org-roam-dailies--capture` `org-roam-dailies-capture-today`. I extended this argument to also be available in other built-in dailies functions, as I didn't see any reason why not and it results in my opinion in more consistent behaviour. The rationale is the same as in #2028: Allow users to add keybindings (or in my case hydras) to calls of org-roam-dailies functions with specific template keys, thus circumventing the selection screen. So far it seems to work for me. I have only one pet-peeve about the interface, if the user starts adding keys to all their goto-functions, they might add (org-roam-dailies-goto-date nil "<key>") Then the key-string will be interpreted as the value for `prefer-future` and since it's non-nil, there won't be an error. [1] https://github.com/org-roam/org-roam/pull/2028	2022-01-29 14:07:19 -08:00
Jethro Kuan	aafe4114c2	(fix)node: make filter-fn for org-roam-node-random optional (#2063 ) Also, make interactive argument actually apply for other-window	2022-01-25 21:54:06 -08:00
Álmos-Ágoston Zediu	3e2716edf3	(fix)node: added DOUBLE ACUTE ACCENT for unicode normalization (#2060 )	2022-01-21 15:50:52 -08:00
Jethro Kuan	445e3594b2	(fix)dailies: remove f require (#2057 )	2022-01-20 15:14:24 -08:00
Jethro Kuan	6f5d65abd9	(breaking!)node: simplify default display-template (#2054 ) Revert to a simplified `org-roam-node-display-template`, because on non-vertical completion frameworks it looks and behaves strangely. To restore the original default behaviour, set `org-roam-node-display-template` in your Emacs configuration as such: (setq org-roam-node-display-template (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag)))	2022-01-20 11:19:41 -08:00
Jethro Kuan	817d8036fb	(fix)capture: return id in setup-target-location (#2052 ) Fixes #2051.	2022-01-19 18:57:07 -08:00
Jethro Kuan	c17310f0de	(feat)org-roam-node-random: support filter-fn (#2050 )	2022-01-19 14:23:57 -08:00
Jethro Kuan	bf3ebe2121	(feat)capture: create ID before capture process (#2049 ) * (feat)capture: create ID before capture process This allows the ID to be used as part of the capture template. Addresses #2048. * update changelog	2022-01-19 13:41:20 -08:00
Jethro Kuan	47ad646d51	(docs)completions: document org-roam-node-display-template (#2047 )	2022-01-18 15:56:47 -08:00
Groobles	6263c3a956	(minor)dailies: fixed some wording (#2045 )	2022-01-17 18:19:39 -08:00
Jethro Kuan	69742c3d51	(feat)db: add customizability of extra element link parsing (#2042 ) Adds two customizable variables: org-roam-db-extra-links-elements and org-roam-db-extra-links-exclude-keys, which govern which elements are to be considered for link parsing by Org-roam. Also added sane defaults to org-roam-db-extra-links-exclude-keys.	2022-01-16 13:30:13 -08:00
Jethro Kuan	5b15159a2c	docs: symlink resolution with find-file-visit-truename <p dir="auto"><span class="issue-keyword tooltipped tooltipped-se" aria-label="This pull request closes issue #1869.">Closes</span> <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1004482400" data-permission-text="Title is private" data-url="https://github.com/org-roam/org-roam/issues/1869" data-hovercard-type="issue" data-hovercard-url="/org-roam/org-roam/issues/1869/hovercard" href="https://github.com/org-roam/org-roam/issues/1869">#1869</a></p>	2022-01-15 21:36:28 -08:00
Stefan Kangas	c0c240b975	(chore): Drop f.el and s.el dependency (#2025 ) Drops the f.el and implicit s.el dependency. Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2022-01-15 21:26:20 -08:00
Andreas Stuhlmüller	001de3a874	(fix): fix completions width for Helm users (#2040 )	2022-01-15 18:24:52 -08:00
Jethro Kuan	6170cc9928	(release): bump 2021 -> 2022, 2.1.0 -> 2.2.0	2022-01-14 10:53:56 -08:00
Jethro Kuan	cc95540135	(fix): hotfix changelog	2022-01-14 10:51:06 -08:00
Jethro Kuan	24a683d58c	(release): 2.2.0 (#2037 )	2022-01-14 10:50:21 -08:00
Nicolas Chachereau	86c9085363	(fix)core: make 'fd and 'fdfind backend work for listing files (#2021 )	2022-01-11 15:05:27 -08:00
Andrey Akulov	b67bccd6c2	(feat)dailies: add `keys` argument to `org-roam-dailies-capture-today` and `org-roam-dailies--capture` (#2028 )	2022-01-11 14:13:40 -08:00
Jethro Kuan	8b43093d1a	(fix)org-roam-with-file: ensure local variables are respected (#2033 ) When visiting a file, ensure that local variables are respected.	2022-01-12 03:38:44 +08:00
Noboru Ota	679ef6ef00	(fix)db: pragma foreign keys to work with sqlite3 (#2018 ) * (fix):db: pragma foreign keys to work with sqlite3 This commit is follow-up for PR #2009 should fix issues #1927 & #1910. Currently, `[:pragma (= foreign_keys ON)]` is present only in function `org-roam-db--init`. This means the `foreign_keys` is turned on only when the db file is created for the first time. Subsequent Emacs sessions won't turn it on as the db file is already present and does not evaluate `org-roam-db--init`. This PRAGMA needs to be turned on each database connection at runtime according to sqlite's documentation (https://sqlite.org/foreignkeys.html#fk_enable) ``` Foreign key constraints are disabled by default (for backwards compatibility), so must be enabled separately for each database connection ``` I have observed that on Windows only the Emacs session that initially creates the Org-roam db file works correctly with the `sqlite3` option. Subsequent Emacs sessions have the same "Unique constraint failed" error messages. I have tested this patch on Windows and Ubuntu; both seem to work in the first and subsequent Emacs sessions. I am not 100% sure if the location of the PRAGMA is the best; use it as a proof-of-cocenpt for the fix. Thank you. * remove: [:pragma (= foreign_keys ON)] from org-roam-db--init * fix: defconst org-roam--sqlite-available-p outputs error When `org-roam-database-connector` is not `sqlite`, it outputs an unnecessary error when Org-roam starts up as `defconst` evaluates `(emacsql-sqlite-ensure-binary)`. ``` Org-roam initialization: (error "No EmacSQL SQLite binary available, aborting") ``` For other database connectors, this is not relevant. * chore: rm org-roam--sqlite-available-p As per our conversation, org-roam--sqlite-available-p not needed.	2022-01-02 14:03:30 +08:00
Bruce D'Arcus	ee9a8d423e	doc: Add mention of org-cite to bibliography (#2015 ) * doc: Add mention of org-cite to bibliography * regenerate texi Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2021-12-27 18:07:27 +08:00
Jethro Kuan	d3c7d74329	(feat)db: allow [cite:@foo] links in ROAM_REFS (#2017 )	2021-12-27 16:05:17 +08:00
lorniu	3bf0a0a35d	Use `locate-user-emacs-file` instead of `expand-file-name`. (#2016 ) Then all advices on `locate-user-emacs-file` will work.	2021-12-27 14:37:46 +08:00
Noboru Ota	d0f17c6477	(docs): correct how to install gcc on Windows (#2013 ) * docs: Correct how to install gcc on Windows PATH needs to be manually set on Windows. Previously, it was explicitly mentioned that it was unnecessary. More recent experience is that it's necessary. * regenerate texi Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2021-12-23 17:22:02 +08:00