(feat!)capture: change id creation to headline on entry-type capture-templates

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)))

.dir-locals.el

@@ -5,9 +5,9 @@
   (elisp-lint-indent-specs . ((describe . 1)
                               (it . 1)
                               (org-element-map . defun)
+                              (org-roam-dolist-with-progress . 2)
                               (org-roam-with-temp-buffer . 1)
                               (org-with-point-at . 1)
                               (magit-insert-section . defun)
                               (magit-section-case . 0)
-                              (->> . 1)
                               (org-roam-with-file . 2)))))

CHANGELOG.md

@@ -1,9 +1,90 @@
 # Changelog
-
-## 1.2.4 (TBD)
+## TBD
+### 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`
+### Removed
+### Fixed
+- [#2055](https://github.com/org-roam/org-roam/pull/2055) dailies: removed stray f require, which was causing require and compilation errors
+- [#2056](https://github.com/org-roam/org-roam/pull/2056) capture: IDs are now created for entries in capture templates
+### Changed
+- [#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
 
+## 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
+- [#1795](https://github.com/org-roam/org-roam/pull/1795) buffer: optimized reflinks fetch
+- [#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
+- [#1693](https://github.com/org-roam/org-roam/pull/1693) added `filter-fn` and `templates` parameter to `org-roam-capture`, `org-roam-node-find`, and `org-roam-node-insert`
+- [#1709](https://github.com/org-roam/org-roam/pull/1709) added ability to specify default value in org-roam capture templates
+- [#1710](https://github.com/org-roam/org-roam/pull/1710) added `org-roam-extract-subtree`
+- [#1720](https://github.com/org-roam/org-roam/pull/1720) added `org-roam-db-update-on-save`
+- [#1758](https://github.com/org-roam/org-roam/pull/1758) added `org-roam-db-autosync-mode`, replacing `org-roam-setup` and `org-roam-teardown`
+
+### Removed
+- [#1716](https://github.com/org-roam/org-roam/pull/1716) helper function `org-roam-get-keyword` is now obsolete: prefer `org-collect-keywords`
+
+### Changed
+- [#1595](https://github.com/org-roam/org-roam/pull/1595), [#1724](https://github.com/org-roam/org-roam/pull/1724) Major refactoring and restructuring of the codebase
+- [#1655](https://github.com/org-roam/org-roam/pull/1655) improved org-roam contents preview
+- [#1741](https://github.com/org-roam/org-roam/pull/1741) expose `org-roam-capture-` keys in interactive commands
+- [#1786](https://github.com/org-roam/org-roam/pull/1786) org-roam-version now outputs commit hash if found
+- [#1788](https://github.com/org-roam/org-roam/pull/1788) the point is not moved if the node is already visited
+
+### Fixed
+- [#1608](https://github.com/org-roam/org-roam/pull/1608) migration: empty ROAM_REFS are now removed
+- [#1609](https://github.com/org-roam/org-roam/pull/1609) migration: fixed file-link replacement
+- [#1653](https://github.com/org-roam/org-roam/pull/1653) migration: fixed tags migration
+- [#1694](https://github.com/org-roam/org-roam/pull/1694) core: nodes with no title are now skipped
+- [#1637](https://github.com/org-roam/org-roam/pull/1637) core: fix org-ref multi-cite links not being split
+- [#1651](https://github.com/org-roam/org-roam/pull/1651) core: fix org-roam-file-p crashing when there is no corresponding file
+- [#1705](https://github.com/org-roam/org-roam/pull/1705) core: fix for add/remove of file-level tags
+- [#1769](https://github.com/org-roam/org-roam/pull/1769) core: gracefully handle absence of `org-id-locations-file`
+- [#1713](https://github.com/org-roam/org-roam/pull/1713) capture: check for file-existence before template insertion
+- [#1725](https://github.com/org-roam/org-roam/pull/1725) db: always compute hash of encrypted file to prevent re-processing of encrypted files
+
+## 2.0.0
+### Added
 - [#1396](https://github.com/org-roam/org-roam/pull/1396) add option to choose between prepending, appending, and omitting `roam_tags` in file completion
 - [#1270](https://github.com/org-roam/org-roam/pull/1270) capture: create OLP if it does not exist. Removes need for OLP setup in `:head`.
 - [#1353](https://github.com/org-roam/org-roam/pull/1353) support file-level property drawers
@@ -11,7 +92,7 @@
 ### Changed
 
 - [#1352](https://github.com/org-roam/org-roam/pull/1352) prefer lower-case for roam_tag and roam_alias in interactive commands
-- [#1513](https://github.com/org-roam/org-roam/pull/1513) replaced hardcoded "svg" with defcustom org-roam-graph-filetype 
+- [#1513](https://github.com/org-roam/org-roam/pull/1513) replaced hardcoded "svg" with defcustom org-roam-graph-filetype
 - [#1540](https://github.com/org-roam/org-roam/pull/1540) allow `roam_tag` and `roam_alias` to be specified on multiple lines
 
 ### Fixed

README.md

@@ -33,38 +33,181 @@ solution for anyone already using Org-mode for their personal wiki.
 
 ## Installation
 
-You can install `org-roam` using `package.el`:
+Down below you will find basic installation instructions for how to quickly
+install `org-roam` using various environments for various purposes. For more
+detailed information, please read the [manual][docs].
+
+### Using `package.el`
+<details>
+<summary>Toggle instructions</summary>
+
+You can install `org-roam` from [MELPA](https://melpa.org/) or [MELPA
+Stable](https://stable.melpa.org/) using `package.el`:
 
 ```
 M-x package-install RET org-roam RET
 ```
+</details>
 
-Here's a sample configuration with `use-package`:
+### Using `straight.el`
+<details>
+<summary>Toggle instructions</summary>
+
+Installation from MELPA or MELPA Stable using `straight.el`:
+
+```emacs-lisp
+(straight-use-package 'org-roam)
+```
+
+Or with `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-setup)
-      ;; If using org-roam-protocol
-      (require 'org-roam-protocol))
+  :straight t
+  ...)
 ```
 
-The `file-truename` function is only necessary when you use symbolic links
-inside `org-roam-directory`: Org-roam does not resolve symbolic links.
+If you need to install the package directly from the source repository, instead
+of from MELPA, the next sample shows how to do so:
 
-Org-roam requires sqlite to function. Org-roam optionally uses Graphviz for
-graph-related functionality. It is recommended to install PCRE-enabled ripgrep
-for better performance and extended functionality.
+```emacs-lisp
+(use-package org-roam
+  :straight (:host github :repo "org-roam/org-roam"
+             :files (:defaults "extensions/*"))
+  ...)
+```
+
+If you plan to use your own local fork for the development and contribution, the
+next sample will get you there:
+
+```emacs-lisp
+(use-package org-roam
+  :straight (:local-repo "/path/to/org-roam-fork"
+             :files (:defaults "extensions/*")
+             :build (:not compile))
+  ...)
+```
+</details>
+
+### Using Doom Emacs
+<details>
+<summary>Toggle instructions</summary>
+
+Doom's `:lang org` module comes with support for `org-roam`, but it's not
+enabled by default. To activate it pass `+roam2` flag to `org` module in your
+`$DOOMDIR/init.el` (e.g. `(org +roam2)`), save the file and run `doom sync -u`
+in your shell.
+
+To provide better stability, Doom pins the package to a specific commit. If you
+need to unpin it *(not recommended doing that, request Doom to bump the package
+instead)* use the next in your `packages.el`:
+
+```emacs-lisp
+(unpin! org-roam)
+```
+
+If for some reasons you want to use a different recipe for `org-roam`, you can
+use the next form in your `packages.el` to install the package from a recipe
+repository (e.g. MELPA):
+
+```emacs-lisp
+(package! org-roam)
+```
+
+You can pass `:pin "commit hash"` to pin the package to a specific commit.
+
+With the next sample you can install the package directly from the source
+repository:
+
+```emacs-lisp
+(package! org-roam
+  :recipe (:host github :repo "org-roam/org-roam"
+           :files (:defaults "extensions/*")))
+```
+
+And if you plan to use your own local fork for the development or contribution,
+the next sample will get you there:
+
+```emacs-lisp
+(package! org-roam
+  :recipe (:local-repo "/path/to/org-roam-fork"
+           :files (:defaults "extensions/*")
+           :build (:not compile)))
+```
+</details>
+
+### Without a package manager
+<details>
+<summary>Toggle instructions</summary>
+
+To install the package without using a package manager you have the next two
+options:
+
+1. Install the package by cloning it with `git` from the source repository.
+2. Or install the package by downloading the latest [release
+   version](https://github.com/org-roam/org-roam/releases).
+   
+In both of the cases you will need to ensure that you have all the required
+dependencies. These include:
+
+- dash
+- f
+- s
+- org (9.4 is the minimal required version!)
+- emacsql
+- emacsql-sqlite
+- magit-section
+- filenotify-recursive
+
+After installing the package, you will need to properly setup `load-path` to the
+package:
+
+``` emacs-lisp
+(add-to-list 'load-path "/path/to/org-roam/")
+(add-to-list 'load-path "/path/to-org-roam/extensions/")
+```
+
+After which you should be able to resolve `(require 'org-roam)` call without any
+problems.
+
+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
+Crafters](https://www.youtube.com/c/SystemCrafters) has produced an introductory
+video that covers the basic commands:
+
+[![Getting Started with Org Roam - Build a Second Brain in Emacs](https://img.youtube.com/vi/AyhPmypHDEw/0.jpg)](https://www.youtube.com/watch?v=AyhPmypHDEw)
 
 ## Getting Help
 
@@ -109,6 +252,6 @@ General Public License, Version 3.
 [release]: https://github.com/org-roam/org-roam/releases
 [docs]: https://www.orgroam.com/manual.html
 [discourse]: https://org-roam.discourse.group/
-[slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
+[slack]: https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ
 [issues]: https://github.com/org-roam/org-roam/issues
 [faq]: https://www.orgroam.com/manual.html#FAQ

default.mk

@@ -44,16 +44,17 @@ HTMLDIRS  = $(PACKAGES)
 PDFFILES  = $(addsuffix .pdf,$(PACKAGES))
 EPUBFILES = $(addsuffix .epub,$(PACKAGES))
 
-ELS = org-roam-buffer.el
+ELS = org-roam.el
 ELS += org-roam-capture.el
 ELS += org-roam-compat.el
-ELS += org-roam-completion.el
-ELS += org-roam-dailies.el
 ELS += org-roam-db.el
-ELS += org-roam.el
-ELS += org-roam-graph.el
-ELS += org-roam-macs.el
-ELS += org-roam-protocol.el
+ELS += org-roam-mode.el
+ELS += org-roam-node.el
+ELS += org-roam-utils.el
+ELS += extensions/org-roam-dailies.el
+ELS += extensions/org-roam-graph.el
+ELS += extensions/org-roam-overlay.el
+ELS += extensions/org-roam-protocol.el
 ELCS = $(ELS:.el=.elc)
 ELMS = org-roam.el $(filter-out $(addsuffix .el,$(PACKAGES)),$(ELS))
 ELGS = org-roam-autoloads.el org-roam-version.el

doc/index.html

@@ -95,7 +95,7 @@
         <ul>
             <li>Read our documentation within Emacs, or on the <a href="https://www.orgroam.com/manual.html">Online Manual</a></li>
             <li>Participate in our forum discussions on <a href="https://org-roam.discourse.group">Discourse</a></li>
-            <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg">Slack</a></li>
+            <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ">Slack</a></li>
           </ul>
       </div>
     </section>
@@ -116,8 +116,8 @@
         <div class="row">
           <a
             class="content footer-links"
-            href="https://github.com/org-roam/org-roam-server"
-            >org-roam-server</a
+            href="https://github.com/org-roam/org-roam-ui"
+            >org-roam-ui</a
           >
         </div>
       </div>
@@ -151,7 +151,7 @@
         <div class="row">
           <a
             class="content footer-links"
-            href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg"
+            href="https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ"
             >Slack</a
           >
         </div>

doc/org-roam.org

@@ -1,20 +1,20 @@
 #+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 2.0.0
+#+subtitle: for version 2.2.0
 
 #+options: H:4 num:3 toc:nil creator:t ':t
 #+property: header-args :eval never
 #+texinfo: @noindent
 
-This manual is for Org-roam version 2.0.0.
+This manual is for Org-roam version 2.2.0.
 
 #+BEGIN_QUOTE
 Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
@@ -67,7 +67,7 @@ Org-roam provides these benefits over other tooling:
 
 Org-roam is a tool that will appear unfriendly to anyone unfamiliar with Emacs
 and Org-mode, but it is also extremely powerful to those willing to put effort
-inn mastering the intricacies. Org-roam stands on the shoulders of giants. Emacs
+in mastering the intricacies. Org-roam stands on the shoulders of giants. Emacs
 was first created in 1976, and remains the tool of choice for many for editing
 text and designing textual interfaces. The malleability of Emacs allowed the
 creation of Org-mode, an all-purpose plain-text system for maintaining TODO
@@ -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 [[id:4eae8552-95e1-4e4a-b7b7-2c53433730ea][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*
@@ -198,17 +198,6 @@ using:
   M-x package-install RET org-roam RET
 #+END_EXAMPLE
 
-** Installing from Apt
-
-Users of Debian 11 or later or Ubuntu 20.10 or later can simply install Org-roam
-using Apt:
-
-#+BEGIN_SRC bash
-  apt-get install elpa-org-roam
-#+END_SRC
-
-Org-roam will then be autoloaded into Emacs.
-
 ** Installing from Source
 
 You may install Org-roam directly from the repository on [[https://github.com/org-roam/org-roam][GitHub]] if you like.
@@ -247,6 +236,7 @@ dependencies that it requires. These include:
 - org
 - emacsql
 - emacsql-sqlite
+- magit-section
 
 You can install this manually as well, or get the latest version from MELPA. You
 may wish to use [[https://github.com/jwiegley/use-package][use-package]], [[https://github.com/raxod502/straight.el][straight.el]] to help manage this.
@@ -298,29 +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. 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:
 
-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:
-   
    #+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-setup~
+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
@@ -383,48 +369,27 @@ 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.
-
-Next, we setup Org-roam to run functions on file changes to maintain cache
-consistency. This is achieved by running ~M-x org-roam-setup~. To ensure that
-Org-roam is available on startup, place this in your Emacs configuration:
+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
-  (require 'org-roam)
-  (org-roam-setup)
+  (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
+ensure that Org-roam is available on startup, place this in your Emacs
+configuration:
+
+#+begin_src emacs-lisp
+(org-roam-db-autosync-mode)
 #+end_src
 
 To build the cache manually, run ~M-x org-roam-db-sync~. Cache builds may
 take a while the first time, but subsequent builds are often instantaneous
 because they only reprocess modified files.
 
-** Customizing Node Caching
-
-By default, all nodes (any headline or file with an ID) are cached by Org-roam.
-There are instances where you may want to have headlines with ID, but not have
-them cached by Org-roam.
-
-To exclude a headline from the Org-roam database, set the ~ROAM_EXCLUDE~
-property to a non-nil value. For example:
-
-#+begin_src org
-,* Foo
-  :PROPERTIES:
-  :ID:       foo
-  :ROAM_EXCLUDE: t
-  :END:
-#+end_src
-
-One can also set ~org-roam-db-node-include-function~. For example, to exclude
-all headlines with the ~ATTACH~ tag from the Org-roam database, one can set:
-
-#+begin_src org
-(setq org-roam-db-node-include-function
-      (lambda ()
-        (not (member "ATTACH" (org-get-tags)))))
-#+end_src
-
-** TODO Creating and Linking Nodes
+** Creating and Linking Nodes
 
 Org-roam makes it easy to create notes and link them together. There are 2 main
 functions for creating nodes:
@@ -451,25 +416,186 @@ node. If you instead entered a title that does not exist, you will once again be
 brought through the node creation process.
 
 One can also conveniently insert links via the completion-at-point functions
-Org-roam provides (see [[id:70083bfd-d1e3-42b9-bf83-5b05708791c0][Completion]]).
+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
+
+Org-roam uses a sqlite database to perform caching, but there are multiple Emacs
+libraries that can be used. The default used by Org-roam is ~emacs-sqlite~.
+Below the pros and cons of each package is used:
+
+[[https://github.com/skeeto/emacsql][**emacs-sqlite**]]
+
+The default option used by Org-roam. This library is the most mature and
+well-supported and is imported by default in Org-roam.
+
+One downside of using ~emacs-sqlite~ is that using it requires compilation and
+can cause issues in some environments (especially Windows). If you have issues
+producing the customized binary required by ~emacs-sqlite~, consider using
+~emacs-sqlite3~.
+
+[[https://github.com/cireu/emacsql-sqlite3][**emacs-sqlite3**]]
+
+~emacs-sqlite3~ uses the official sqlite3 binary that can be obtained from your
+system's package manager. This is useful if you have issues producing the
+~sqlite3~ binary required by the other packages. However, it is not recommended
+because it has some compatibility issues with Emacs, but should work for most
+regular cases. See [[https://nullprogram.com/blog/2014/02/06/][Chris Wellon's blog post]] for more information.
+
+To use ~emacsql-sqlite3~, ensure that the package is installed, and set:
+
+#+begin_src emacs-lisp
+  (setq org-roam-database-connector 'sqlite3)
+#+end_src
+
+[[https://github.com/emacscollective/emacsql-libsqlite3/][**emacsql-libsqlite3**]]
+
+~emacs-libsqlite3~ is a relatively young package which uses an Emacs module that
+exposes parts of the SQLite C API to Emacs Lisp, instead of using subprocess as
+~emacsql-sqlite~ does. It is expected to be a more performant drop-in
+replacement for ~emacs-sqlite~.
+
+At the moment it is experimental and does not work well with the SQL query load
+required by Org-roam, but you may still try it by ensuring the package is
+installed and setting:
+
+#+begin_src emacs-lisp
+  (setq org-roam-database-connector 'libsqlite3)
+#+end_src
+
+** What to cache
+
+By default, all nodes (any headline or file with an ID) are cached by Org-roam.
+There are instances where you may want to have headlines with ID, but not have
+them cached by Org-roam.
+
+To exclude a headline from the Org-roam database, set the ~ROAM_EXCLUDE~
+property to a non-nil value. For example:
+
+#+begin_src org
+,* Foo
+  :PROPERTIES:
+  :ID:       foo
+  :ROAM_EXCLUDE: t
+  :END:
+#+end_src
+
+One can also set ~org-roam-db-node-include-function~. For example, to exclude
+all headlines with the ~ATTACH~ tag from the Org-roam database, one can set:
+
+#+begin_src org
+(setq org-roam-db-node-include-function
+      (lambda ()
+        (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
+and saved, it updates the database for the corresponding file. This keeps the
+database up-to-date, causing the least surprise when using the interactive
+commands.
+
+However, depending on how large your Org files are, database updating can be a
+slow operation. You can disable the automatic updating of the database by
+setting ~org-roam-db-update-on-save~ to ~nil~.
+
+- Variable: org-roam-db-update-on-save
+
+If t, update the Org-roam database upon saving the file. Disable this if your
+files are large and updating the database is slow.
 
 * The Org-roam Buffer
 
 Org-roam provides the Org-roam buffer: an interface to view relationships with
 other notes (backlinks, reference links, unlinked references etc.). There are
-two main functions to use here:
+two main commands to use here:
 
-- ~org-roam-buffer~: Launch an Org-roam buffer for the current node at point.
 - ~org-roam-buffer-toggle~: Launch an Org-roam buffer that tracks the node
   currently at point. This means that the content of the buffer changes as the
   point is moved, if necessary.
-
-Use ~org-roam-buffer-toggle~ when you want wish for the Org-roam buffer to
-buffer, call ~M-x org-roam-buffer~.
-
-- Function: org-roam-buffer
-
-  Launch an Org-roam buffer for the current node at point.
+- ~org-roam-buffer-display-dedicated~: Launch an Org-roam buffer for a specific
+  node without visiting its file. Unlike ~org-roam-buffer-toggle~ you can have
+  multiple such buffers and their content won't be automatically replaced with a
+  new node at point.
 
 To bring up a buffer that tracks the current node at point, call ~M-x
 org-roam-buffer-toggle~.
@@ -478,6 +604,13 @@ org-roam-buffer-toggle~.
 
   Toggle display of the ~org-roam-buffer~.
 
+To bring up a buffer that's dedicated for a specific node, call ~M-x
+org-roam-buffer-display-dedicated~.
+
+- Function: org-roam-buffer-display-dedicated
+
+  Launch node dedicated Org-roam buffer without visiting the node itself.
+
 ** Navigating the Org-roam Buffer
 
 The Org-roam buffer uses ~magit-section~, making the typical ~magit-section~
@@ -485,10 +618,10 @@ keybindings available. Here are several of the more useful ones:
 
 - ~M-{N}~: ~magit-section-show-level-{N}-all~
 - ~n~: ~magit-section-forward~
--~<TAB>~: ~magit-section-toggle~
-- ~<RET>~: ~org-roam-visit-thing~
+- ~<TAB>~: ~magit-section-toggle~
+- ~<RET>~: ~org-roam-buffer-visit-thing~
 
-~org-roam-visit-thing~ is a placeholder command, that is replaced by
+~org-roam-buffer-visit-thing~ is a placeholder command, that is replaced by
 section-specific commands such as ~org-roam-node-visit~.
 
 ** Configuring what is displayed in the buffer
@@ -500,10 +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-sections~.
+To configure what sections are displayed in the buffer, set ~org-roam-mode-section-functions~.
 
 #+begin_src emacs-lisp
-  (setq org-roam-mode-sections
+  (setq org-roam-mode-section-functions
         (list #'org-roam-backlinks-section
               #'org-roam-reflinks-section
               ;; #'org-roam-unlinked-references-section
@@ -636,10 +769,60 @@ Org-roam also provides some functions to add or remove refs.
 
   Remove a ref from the node at point.
 
-* Completion
+* Citations
+
+Since version 9.5, Org has first-class support for citations. Org-roam supports
+the caching of both these in-built citations (of form ~[cite:@key]~) and [[https://github.com/jkitchin/org-ref][org-ref]]
+citations (of form cite:key).
+
+Org-roam attempts to load both the ~org-ref~ and ~org-cite~ package when
+indexing files, so no further setup from the user is required for citation
+support.
+
+** Using the Cached Information
+
+It is common to use take reference notes for academic papers. To designate the
+node to be the canonical node for the academic paper, we can use its unique
+citation key:
+
+#+begin_src org
+,* Probabilistic Robotics
 :PROPERTIES:
-:ID:       70083bfd-d1e3-42b9-bf83-5b05708791c0
+:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
+:ROAM_REFS: @thrun2005probabilistic
 :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
+,* Probabilistic Robotics
+:PROPERTIES:
+:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
+:ROAM_REFS: cite:thrun2005probabilistic
+:END:
+#+end_src
+
+for ~org-ref~.
+
+When another node has a citation for that key, we can see it using the
+~Reflinks~ section of the Org-roam buffer.
+
+Extension developers may be interested in retrieving the citations within their
+notes. This information can be found within the ~citation~ table of the Org-roam
+database.
+
+* Completion
 
 Completions for Org-roam are provided via ~completion-at-point~. Org-roam
 currently provides completions in two scenarios:
@@ -691,7 +874,7 @@ extension in your Org-roam capture templates. For example:
 
 #+begin_src emacs-lisp
 (setq org-roam-capture-templates '(("d" "default" plain "%?"
-     :if-new (file+head "${slug}.org.gpg"
+     :target (file+head "${slug}.org.gpg"
                         "#+title: ${title}\n")
      :unnarrowed t)))
 #+end_src
@@ -814,6 +997,29 @@ defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandle
 
 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:
 
@@ -847,7 +1053,7 @@ graph navigable.
 
 ** The roam-ref protocol
 
-This protocol finds or creates a new note with a given ~roam_key~:
+This protocol finds or creates a new note with a given ~ROAM_REFS~:
 
 [[file:images/roam-ref.gif]]
 
@@ -871,8 +1077,7 @@ or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
 #+END_SRC
 
 where ~template~ is the template key for a template in
-~org-roam-capture-ref-templates~ (see [[*The Templating System][The Templating System]]). These templates
-should contain a ~#+roam_key: ${ref}~ in it.
+~org-roam-capture-ref-templates~ (see [[*The Templating System][The Templating System]]).
 
 * The Templating System
 
@@ -888,12 +1093,12 @@ will be no prompt for template selection.
 ** Template Walkthrough
 
 To demonstrate the additions made to org-capture templates. Here, we explain
-the default template, reproduced below. You will find some most of the elements
+the default template, reproduced below. You will find most of the elements
 of the template are similar to ~org-capture~ templates.
 
 #+BEGIN_SRC emacs-lisp
 (("d" "default" plain "%?"
-  :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+  :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
                      "#+title: ${title}\n")
   :unnarrowed t))
 #+END_SRC
@@ -907,8 +1112,12 @@ of the template are similar to ~org-capture~ templates.
    here.
 5. ~"%?"~ is the template inserted on each call to ~org-roam-capture-~.
    This template means don't insert any content, but place the cursor here.
-6. ~:if-new~ is a compulsory specification in the Org-roam capture template.
-   This indicates the location for the new node.
+6. ~:target~ is a compulsory specification in the Org-roam capture template. The
+   first element of the list indicates the type of the target, the second
+   element indicates the location of the captured node, and the rest of the
+   elements indicate prefilled template that will be inserted and the position
+   of the point will be adjusted for. The latter behavior varies from type to
+   type of the capture target.
 7. ~:unnarrowed t~ tells org-capture to show the contents for the whole file,
    rather than narrowing to just the entry. This is part of the Org-capture
    templates.
@@ -933,6 +1142,23 @@ strings. ~${foo}~'s substitution is performed as follows:
 3. Else look up ~org-roam-capture--info~ for ~foo~. This is an internal variable
    that is set before the capture process begins.
 4. If none of the above applies, read a string using ~completing-read~.
+   a. Org-roam also provides the ~${foo=default_val}~ syntax, where if a default
+      value is provided, will be the initial value for the ~foo~ key during
+      minibuffer completion.
+
+One can check the list of available keys for nodes by inspecting the
+~org-roam-node~ struct. At the time of writing, it is:
+
+#+begin_src emacs-lisp
+  (cl-defstruct (org-roam-node (:constructor org-roam-node-create)
+                               (:copier nil))
+    "A heading or top level file with an assigned ID property."
+    file file-hash file-atime file-mtime
+    id level point todo priority scheduled deadline title properties olp
+    tags aliases refs)
+#+end_src
+
+This makes ~${file}~, ~${file-hash}~ etc. all valid substitutions.
 
 * Graphing
 
@@ -969,10 +1195,10 @@ ARG may be any of the following values:
   2. a function accepting a single argument: the graph file path.
 
   ~nil~ uses ~view-file~ to view the graph.
-  
+
   If you are using WSL2 and would like to open the graph in Windows, you can use
   the second option to set the browser and network file path:
-  
+
   #+BEGIN_SRC emacs-lisp
   (setq org-roam-graph-viewer
       (lambda (file)
@@ -1007,9 +1233,6 @@ for customizable options.
   Example: ~'(("dir" . "back"))~
 
 * Org-roam Dailies
-:PROPERTIES:
-:ID:       4eae8552-95e1-4e4a-b7b7-2c53433730ea
-:END:
 
 Org-roam provides journaling capabilities akin to
 Org-journal with ~org-roam-dailies~.
@@ -1034,7 +1257,7 @@ Here is a sane default configuration:
 (setq org-roam-dailies-capture-templates
       '(("d" "default" entry
          "* %?"
-         :if-new (file+head "%<%Y-%m-%d>.org"
+         :target (file+head "%<%Y-%m-%d>.org"
                             "#+title: %<%Y-%m-%d>\n"))))
 #+end_src
 
@@ -1073,7 +1296,7 @@ There are also commands which allow you to use Emacs’s ~calendar~ to find the
   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.
 
@@ -1220,12 +1443,15 @@ 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~.
 
 For example, though helm-bibtex provides the ability to visit notes for
 bibliographic entries, org-roam-bibtex extends it with the ability to visit the
-file with the right =#+ROAM_KEYS=.
+file with the right ~ROAM_REFS~.
 
 ** Spaced Repetition
 
@@ -1247,20 +1473,27 @@ variable using directory-local variables. This is what ~.dir-locals.el~ may
 contain:
 
 #+BEGIN_SRC emacs-lisp
-  ((nil . ((org-roam-directory . (expand-file-name "."))
-           (org-roam-db-location . (expand-file-name "./org-roam.db")))))
+  ((nil . ((org-roam-directory . "/path/to/alt/org-roam-dir")
+           (org-roam-db-location . "/path/to/alt/org-roam-dir/org-roam.db"))))
+#+END_SRC
+
+Note ~org-roam-directory~ and ~org-roam-db-location~ should be an absolute path, not relative.
+
+Alternatively, use ~eval~ if you wish to call functions:
+
+#+BEGIN_SRC emacs-lisp
+  ((nil . ((eval . (setq-local
+                    org-roam-directory (expand-file-name (locate-dominating-file
+                                                          default-directory ".dir-locals.el"))))
+           (eval . (setq-local
+                    org-roam-db-location (expand-file-name "org-roam.db"
+                                                           org-roam-directory))))))
 #+END_SRC
 
 All files within that directory will be treated as their own separate set of
 Org-roam files. Remember to run ~org-roam-db-sync~ from a file within
 that directory, at least once.
 
-** How do I migrate from Roam Research?
-
-Fabio has produced a command-line tool that converts markdown files exported
-from Roam Research into Org-roam compatible markdown. More instructions are
-provided [[https://github.com/fabioberger/roam-migration][in the repository]].
-
 ** How do I create a note whose title already matches one of the candidates?
 
 This situation arises when, for example, one would like to create a note titled
@@ -1273,29 +1506,119 @@ are the solutions:
   set ~ivy-use-selectable-prompt~ to ~t~, so that "bar" is now selectable.
 - Helm :: Org-roam should provide a selectable "[?] bar" candidate at the top of
   the candidate list.
+** How can I stop Org-roam from creating IDs everywhere?
 
-* Migrating from Org-roam v1
+Other than the interactive commands that Org-roam provides, Org-roam does not
+create IDs everywhere. If you are noticing that IDs are being created even when
+you don't want them to be (e.g. when tangling an Org file), check the value you
+have set for ~org-id-link-to-org-use-id~: setting it to ~'create-if-interactive~
+is a popular option.
+
+** How do I migrate from Roam Research?
+
+Fabio has produced a command-line tool that converts markdown files exported
+from Roam Research into Org-roam compatible markdown. More instructions are
+provided [[https://github.com/fabioberger/roam-migration][in the repository]].
+
+** How to migrate from Org-roam v1?
 
 Those coming from Org-roam v1 will do well treating v2 as entirely new software.
 V2 has a smaller core and fewer moving parts, while retaining the bulk of its
 functionality. It is recommended to read the documentation above about nodes.
 
-It is still desirable to migrate notes collected in v1 to v2. To migrate your v1
-notes to v2, you may use the migration script provided in [[https://gist.github.com/jethrokuan/02f41028fb4a6f81787dc420fb99b6e4][this gist]], or [[https://gist.github.com/jethrokuan/02f41028fb4a6f81787dc420fb99b6e4#gistcomment-3737019][this
-gist]], the latter being better tested. [[https://d12frosted.io/posts/2021-06-11-path-to-org-roam-v2.html][This blog post]] provides a good overview of
-what's new in v2 and how to migrate.
+It is still desirable to migrate notes collected in v1 to v2.
+To migrate your v1 notes to v2, use =M-x org-roam-migrate-wizard=.
+[[https://d12frosted.io/posts/2021-06-11-path-to-org-roam-v2.html][This blog post]]
+provides a good overview of what's new in v2 and how to migrate.
 
-Simply put, to migrate notes from v1 to v2, one must:
+Essentially, to migrate notes from v1 to v2, one must:
 
-1. Add IDs to all existing notes. These are located in top-level property
-   drawers (Although note that in v2, not all files need to have IDs)
+1. Add IDs to all existing notes.
+   These are located in top-level property drawers
+   (Although note that in v2, not all files need to have IDs).
 2. Update the Org-roam database to conform to the new schema.
 3. Replace ~#+ROAM_KEY~ into the ~ROAM_REFS~ property
 4. Replace ~#+ROAM_ALIAS~ into the ~ROAM_ALIASES~ property
-5. Move ~#+ROAM_TAGS~ into the ~#+FILETAGS~ property for file-level nodes, and
-   the ~ROAM_TAGS~ property for headline nodes
+5. Move ~#+ROAM_TAGS~ into the ~#+FILETAGS~ property for file-level nodes,
+   and the ~ROAM_TAGS~ property for headline nodes
 6. Replace existing file links with ID links.
 
+** How do I publish my notes with an Internet-friendly graph?
+
+The default graph builder creates a graph with an [[https://orgmode.org/worg/org-contrib/org-protocol.html][org-protocol]]
+handler which is convenient when you're working locally but
+inconvenient when you want to publish your notes for remote access.
+Likewise, it defaults to displaying the graph in Emacs which has the
+exact same caveats.  This problem is solvable in the following way
+using org-mode's native [[https://orgmode.org/manual/Publishing.html][publishing]] capability:
+
+1. configure org-mode to publish your org-roam notes as a project.
+2. create a function that overrides the default org-protocol link
+   creation function(=org-roam-default-link-builder=).
+3. create a hook that's called at the end of graph creation to copy
+   the generated graph to the appropriate place.
+
+The example code below is used to publish to a local directory where a
+separate shell script copies the files to the remote site.
+
+*** Configure org-mode for publishing
+This has two steps:
+1. Setting of a /roam/ project that publishes your notes.
+2. Configuring the /sitemap.html/ generation.
+3. Setting up =org-publish= to generate the graph.
+  
+This will require code like the following:
+#+begin_src emacs-lisp
+  (defun roam-sitemap (title list)
+    (concat "#+OPTIONS: ^:nil author:nil html-postamble:nil\n"
+            "#+SETUPFILE: ./simple_inline.theme\n"
+            "#+TITLE: " title "\n\n"
+            (org-list-to-org list) "\nfile:sitemap.svg"))
+
+  (setq my-publish-time 0)   ; see the next section for context
+  (defun roam-publication-wrapper (plist filename pubdir)
+    (org-roam-graph)
+    (org-html-publish-to-html plist filename pubdir)
+    (setq my-publish-time (cadr (current-time))))
+
+  (setq org-publish-project-alist
+    '(("roam"
+       :base-directory "~/roam"
+       :auto-sitemap t
+       :sitemap-function roam-sitemap
+       :sitemap-title "Roam notes"
+       :publishing-function roam-publication-wrapper
+       :publishing-directory "~/roam-export"
+       :section-number nil
+       :table-of-contents nil
+       :style "<link rel=\"stylesheet\" href=\"../other/mystyle.cs\" type=\"text/css\">")))
+#+end_src
+
+*** Overriding the default link creation function
+The code below will generate a link to the generated html file instead
+of the default org-protocol link.
+#+begin_src emacs-lisp
+  (defun org-roam-custom-link-builder (node)
+    (let ((file (org-roam-node-file node)))
+      (concat (file-name-base file) ".html")))
+
+  (setq org-roam-graph-link-builder 'org-roam-custom-link-builder)
+#+end_src
+
+*** Copying the generated file to the export directory
+The default behavior of =org-roam-graph= is to generate the graph and
+display it in Emacs.  There is an =org-roam-graph-generation-hook=
+available that provides access to the file names so they can be copied
+to the publishing directory.  Example code follows:
+
+#+begin_src emacs-lisp
+  (add-hook 'org-roam-graph-generation-hook
+            (lambda (dot svg) (if (< (- (cadr (current-time)) my-publish-time) 5)
+                                  (progn (copy-file svg "~/roam-export/sitemap.svg" 't)
+                                         (kill-buffer (file-name-nondirectory svg))
+                                         (setq my-publish-time 0)))))
+#+end_src
+
 * Developer's Guide to Org-roam
 ** Org-roam's Design Principle
 
@@ -1383,7 +1706,7 @@ method to access nodes is ~org-roam-node-at-point~ and ~org-roam-node-read~:
   is a function to filter out nodes: it takes a single argument (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-sort-by-file-mtime~
+  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.
 
@@ -1415,7 +1738,7 @@ instead. The exposed function to be used in extensions is ~org-roam-capture-~:
 
   Main entry point.
   GOTO and KEYS correspond to `org-capture' arguments.
-  INFO is an alist for filling up Org-roam's capture templates.
+  INFO is a plist for filling up Org-roam's capture templates.
   NODE is an `org-roam-node' construct containing information about the node.
   PROPS is a plist containing additional Org-roam properties for each template.
   TEMPLATES is a list of org-roam templates.
@@ -1499,7 +1822,7 @@ see the list.
 paren and run =M-x eval-last-sexp RET= or 2) Press =C-c C-c= with your cursor in
 an Org file code block (like =#+BEGIN_SRC emacs-lisp=).
 [fn:roam] To understand more about Roam, a collection of links are available in [[*Note-taking Workflows][Note-taking Workflows]].
- 
+
 # Local Variables:
 # eval: (require 'ol-info)
 # eval: (require 'ox-texinfo+ nil t)

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 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 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: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -29,27 +29,24 @@
 
 ;;; Commentary:
 ;;
-;; This library provides functionality for creating daily-notes. This is a
-;; concept borrowed from Roam Research.
+;; This extension provides functionality for creating daily-notes, or shortly
+;; "dailies". Dailies implemented here as a unique node per unique file, where
+;; 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 or whatever else you can think of.
 ;;
 ;;; Code:
-;;; Library Requires
-(require 'org-capture)
-(require 'org-roam-capture)
-(require 'f)
+(require 'dash)
+(require 'org-roam)
 
-;;;; Declarations
-(defvar org-roam-directory)
-(defvar org-roam-file-extensions)
-(declare-function org-roam-file-p        "org-roam")
-
-;;;; Faces
+;;; Faces
 (defface org-roam-dailies-calendar-note
   '((t :inherit (org-link) :underline nil))
   "Face for dates with a daily-note in the calendar."
   :group 'org-roam-faces)
 
-;;;; Customizable variables
+;;; Options
 (defcustom org-roam-dailies-directory "daily/"
   "Path to daily-notes.
 This path is relative to `org-roam-directory'."
@@ -64,9 +61,11 @@ This path is relative to `org-roam-directory'."
 (defcustom org-roam-dailies-capture-templates
   `(("d" "default" entry
      "* %?"
-     :if-new (file+head "%<%Y-%m-%d>.org"
+     :target (file+head "%<%Y-%m-%d>.org"
                         "#+title: %<%Y-%m-%d>\n")))
   "Capture templates for daily-notes in Org-roam.
+Note that for daily files to show up in the calendar, they have to be of format
+\"org-time-string.org\".
 See `org-roam-capture-templates' for the template documentation."
   :group 'org-roam
   :type '(repeat
@@ -92,7 +91,7 @@ See `org-roam-capture-templates' for the template documentation."
                                       (function :tag "Template function")))
                         (plist :inline t
                                ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :if-new)
+                               :options (((const :format "%v " :target)
                                           (choice :tag "Node location"
                                                   (list :tag "File"
                                                         (const :format "" file)
@@ -127,43 +126,17 @@ See `org-roam-capture-templates' for the template documentation."
                                          ((const :format "%v " :table-line-pos) (string))
                                          ((const :format "%v " :kill-buffer) (const t))))))))
 
+;;; Commands
+;;;; Today
 ;;;###autoload
-(defun org-roam-dailies-find-directory ()
-  "Find and open `org-roam-dailies-directory'."
-  (interactive)
-  (find-file (expand-file-name org-roam-dailies-directory org-roam-directory)))
-
-(defun org-roam-dailies--daily-note-p (&optional file)
-  "Return t if FILE is an Org-roam daily-note, nil otherwise.
-If FILE is not specified, use the current buffer's file-path."
-  (when-let ((path (expand-file-name
-                    (or file
-                        (buffer-file-name (buffer-base-buffer)))))
-             (directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
-    (setq path (expand-file-name path))
-    (save-match-data
-      (and
-       (org-roam-file-p path)
-       (f-descendant-of-p path directory)))))
-
-(defun org-roam-dailies--capture (time &optional goto)
-  "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)))
-    (org-roam-capture- :goto (when goto '(4))
-                       :node (org-roam-node-create)
-                       :templates org-roam-dailies-capture-templates
-                       :props (list :override-default-time time)))
-  (when goto (run-hooks 'org-roam-dailies-find-file-hook)))
-
-;;;; 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 ()
@@ -171,7 +144,7 @@ When GOTO is non-nil, go the note without creating an entry."
   (interactive)
   (org-roam-dailies-capture-today t))
 
-;;; Tomorrow
+;;;; Tomorrow
 ;;;###autoload
 (defun org-roam-dailies-capture-tomorrow (n &optional goto)
   "Create an entry in the daily-note for tomorrow.
@@ -192,7 +165,7 @@ future."
   (interactive "p")
   (org-roam-dailies-capture-tomorrow n t))
 
-;;; Yesterday
+;;;; Yesterday
 ;;;###autoload
 (defun org-roam-dailies-capture-yesterday (n &optional goto)
   "Create an entry in the daily-note for yesteday.
@@ -212,31 +185,7 @@ future."
   (interactive "p")
   (org-roam-dailies-capture-tomorrow (- n) t))
 
-;;; Calendar
-(defun org-roam-dailies-calendar--file-to-date (&optional file)
-  "Convert FILE to date.
-Return (MONTH DAY YEAR)."
-  (let ((file (or file
-                  (buffer-base-buffer (buffer-file-name)))))
-    (cl-destructuring-bind (_ _ _ d m y _ _ _)
-        (org-parse-time-string
-         (file-name-sans-extension
-          (file-name-nondirectory file)))
-      (list m d y))))
-
-(defun org-roam-dailies-calendar--date-to-time (date)
-  "Convert DATE as returned from then calendar (MONTH DAY YEAR) to a time."
-  (encode-time 0 0 0 (nth 1 date) (nth 0 date) (nth 2 date)))
-
-(defun org-roam-dailies-calendar-mark-entries ()
-  "Mark days in the calendar for which a daily-note is present."
-  (when (file-exists-p (expand-file-name org-roam-dailies-directory org-roam-directory))
-    (dolist (date (mapcar #'org-roam-dailies-calendar--file-to-date
-                          (org-roam-dailies--list-files)))
-      (when (calendar-date-is-visible-p date)
-        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
-
-;;; Date
+;;;; Date
 ;;;###autoload
 (defun org-roam-dailies-capture-date (&optional goto prefer-future)
   "Create an entry in the daily-note for a date using the calendar.
@@ -245,9 +194,9 @@ With a `C-u' prefix or when GOTO is non-nil, go the note without
 creating an entry."
   (interactive "P")
   (let ((time (let ((org-read-date-prefer-future prefer-future))
-                (org-read-date t t nil (if goto
-                                           "Find daily-note: "
-                                         "Capture to daily-note: ")))))
+                (org-read-date nil t nil (if goto
+                                             "Find daily-note: "
+                                           "Capture to daily-note: ")))))
     (org-roam-dailies--capture time goto)))
 
 ;;;###autoload
@@ -257,20 +206,7 @@ Prefer past dates, unless PREFER-FUTURE is non-nil."
   (interactive)
   (org-roam-dailies-capture-date t prefer-future))
 
-;;; Navigation
-(defun org-roam-dailies--list-files (&rest extra-files)
-  "List all files in `org-roam-dailies-directory'.
-EXTRA-FILES can be used to append extra files to the list."
-  (let ((dir (expand-file-name org-roam-dailies-directory org-roam-directory))
-        (regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
-    (append (--remove (let ((file (file-name-nondirectory it)))
-                        (when (or (auto-save-file-name-p file)
-                                  (backup-file-name-p file)
-                                  (string-match "^\\." file))
-                          it))
-                      (directory-files-recursively dir regexp))
-            extra-files)))
-
+;;;; Navigation
 (defun org-roam-dailies-goto-next-note (&optional n)
   "Find next daily-note.
 
@@ -308,10 +244,87 @@ negative, find note N days in the future."
   (let ((n (if n (- n) -1)))
     (org-roam-dailies-goto-next-note n)))
 
+(defun org-roam-dailies--list-files (&rest extra-files)
+  "List all files in `org-roam-dailies-directory'.
+EXTRA-FILES can be used to append extra files to the list."
+  (let ((dir (expand-file-name org-roam-dailies-directory org-roam-directory))
+        (regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
+    (append (--remove (let ((file (file-name-nondirectory it)))
+                        (when (or (auto-save-file-name-p file)
+                                  (backup-file-name-p file)
+                                  (string-match "^\\." file))
+                          it))
+                      (directory-files-recursively dir regexp))
+            extra-files)))
+
+(defun org-roam-dailies--daily-note-p (&optional file)
+  "Return t if FILE is an Org-roam daily-note, nil otherwise.
+If FILE is not specified, use the current buffer's file-path."
+  (when-let ((path (expand-file-name
+                    (or file
+                        (buffer-file-name (buffer-base-buffer)))))
+             (directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
+    (setq path (expand-file-name path))
+    (save-match-data
+      (and
+       (org-roam-file-p path)
+       (org-roam-descendant-of-p path directory)))))
+
+;;;###autoload
+(defun org-roam-dailies-find-directory ()
+  "Find and open `org-roam-dailies-directory'."
+  (interactive)
+  (find-file (expand-file-name org-roam-dailies-directory org-roam-directory)))
+
+;;; Calendar integration
+(defun org-roam-dailies-calendar--file-to-date (file)
+  "Convert FILE to date.
+Return (MONTH DAY YEAR) or nil if not an Org time-string."
+  (ignore-errors
+    (cl-destructuring-bind (_ _ _ d m y _ _ _)
+        (org-parse-time-string
+         (file-name-sans-extension
+          (file-name-nondirectory file)))
+      (list m d y))))
+
+(defun org-roam-dailies-calendar-mark-entries ()
+  "Mark days in the calendar for which a daily-note is present."
+  (when (file-exists-p (expand-file-name org-roam-dailies-directory org-roam-directory))
+    (dolist (date (remove nil
+                          (mapcar #'org-roam-dailies-calendar--file-to-date
+                                  (org-roam-dailies--list-files))))
+      (when (calendar-date-is-visible-p date)
+        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
+
 (add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar-mark-entries)
 (add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar-mark-entries)
 
-;;;; Bindings
+;;; Capture implementation
+(add-to-list 'org-roam-capture--template-keywords :override-default-time)
+
+(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.
+
+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-capture- :goto (when goto '(4))
+                       :keys keys
+                       :node (org-roam-node-create)
+                       :templates org-roam-dailies-capture-templates
+                       :props (list :override-default-time time)))
+  (when goto (run-hooks 'org-roam-dailies-find-file-hook)))
+
+(add-hook 'org-roam-capture-preface-hook #'org-roam-dailies--override-capture-time-h)
+
+(defun org-roam-dailies--override-capture-time-h ()
+  "Override the `:default-time' with the time from `:override-default-time'."
+  (when (org-roam-capture--get :override-default-time)
+    (org-capture-put :default-time (org-roam-capture--get :override-default-time)))
+  nil)
+
+;;; Bindings
 (defvar org-roam-dailies-map (make-sparse-keymap)
   "Keymap for `org-roam-dailies'.")
 

extensions/org-roam-graph.el

@@ -1,12 +1,12 @@
-;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-roam-graph.el --- Basic graphing functionality for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020-2021 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: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,18 +27,14 @@
 
 ;;; Commentary:
 ;;
-;; This library provides graphing functionality for org-roam.
+;; This extension implements capability to build and generate graphs in Org-roam
+;; with the help of Graphviz.
 ;;
 ;;; Code:
 (require 'xml) ;xml-escape-string
-(eval-and-compile
-  (require 'org-roam-macs))
-(require 'org-roam-db)
+(require 'org-roam)
 
-;;;; Declarations
-(defvar org-roam-directory)
-
-;;;; Options
+;;; Options
 (defcustom org-roam-graph-viewer (executable-find "firefox")
   "Method to view the org-roam graph.
 It may be one of the following:
@@ -85,7 +81,7 @@ Example:
                ("fillcolor"  . "#EEEEEE")
                ("color"      . "#C9C9C9")
                ("fontcolor"  . "#0A97A6")))
-    ("https" . (("shape"      . "rounded,filled")
+    ("https" . (("style"      . "rounded,filled")
                 ("fillcolor"  . "#EEEEEE")
                 ("color"      . "#C9C9C9")
                 ("fontcolor"  . "#0A97A6"))))
@@ -117,54 +113,78 @@ All other values including nil will have no effect."
           (const :tag "no" nil))
   :group 'org-roam)
 
-(defun org-roam-graph--dot-option (option &optional wrap-key wrap-val)
-  "Return dot string of form KEY=VAL for OPTION cons.
-If WRAP-KEY is non-nil it wraps the KEY.
-If WRAP-VAL is non-nil it wraps the VAL."
-  (concat wrap-key (car option) wrap-key
-          "="
-          wrap-val (cdr option) wrap-val))
+(defcustom org-roam-graph-link-builder 'org-roam-org-protocol-link-builder
+  "Function used to build the Org-roam graph links.
+Given a node name, return a string to be used for the link fed to
+the graph generation utility."
+  :type 'function
+  :group 'org-roam)
 
-(defun org-roam-graph--connected-component (id distance)
-  "Return the edges for all nodes reachable from/connected to ID.
-DISTANCE is the maximum distance away from the root node."
-  (let* ((query
-          (if (= distance 0)
-              "
-WITH RECURSIVE
-  links_of(source, dest) AS
-  (SELECT source, dest FROM links UNION
-   SELECT dest, source FROM links),
-   connected_component(source) AS
-  (SELECT dest FROM links_of WHERE source = $s1 UNION
-   SELECT dest FROM links_of JOIN connected_component USING(source))
-SELECT source, dest, type FROM links WHERE source IN connected_component OR dest IN connected_component;"
-            "
-WITH RECURSIVE
-  links_of(source, dest) AS
-  (SELECT source, dest FROM links UNION
-   SELECT dest, source FROM links),
-  connected_component(source, trace) AS
-  (VALUES ($s1 , json_array($s1)) UNION
-   SELECT lo.dest, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.dest) FROM
-   connected_component AS cc JOIN links_of AS lo USING(source)
-   WHERE (
-    -- Avoid cycles by only visiting each node once.
-    (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.dest) == 0
-    -- Note: BFS is cut off early here.
-    AND json_array_length(cc.trace) < $s2)),
-  nodes(source) as (SELECT DISTINCT source
-   FROM connected_component GROUP BY source ORDER BY min(json_array_length(trace)))
-SELECT source, dest, type FROM links WHERE source IN nodes OR dest IN nodes;")))
-    (org-roam-db-query query id distance)))
+(defcustom org-roam-graph-generation-hook nil
+  "Functions to run after the graph has been generated.
+Each function is called with two arguments: the filename
+containing the graph generation tool, and the generated graph."
+  :type 'hook
+  :group 'org-roam)
+
+(defun org-roam-org-protocol-link-builder (node)
+  "Default org-roam link builder.  Generate an org-protocol link using NODE."
+  (concat "org-protocol://roam-node?node="
+          (url-hexify-string (org-roam-node-id node))))
+
+;;; Interactive command
+;;;###autoload
+(defun org-roam-graph (&optional arg node)
+  "Build and possibly display a graph for NODE.
+ARG may be any of the following values:
+  - nil       show the graph.
+  - `\\[universal-argument]'     show the graph for NODE.
+  - `\\[universal-argument]' N   show the graph for NODE limiting nodes to N steps."
+  (interactive
+   (list current-prefix-arg
+         (and current-prefix-arg
+              (org-roam-node-at-point 'assert))))
+  (let ((graph (cl-typecase arg
+                 (null (org-roam-graph--dot nil 'all-nodes))
+                 (cons (org-roam-graph--dot (org-roam-graph--connected-component
+                                             (org-roam-node-id node) 0)))
+                 (integer (org-roam-graph--dot (org-roam-graph--connected-component
+                                                (org-roam-node-id node) (abs arg)))))))
+    (org-roam-graph--build graph #'org-roam-graph--open)))
+
+;;; Generation and Build process
+(defun org-roam-graph--build (graph &optional callback)
+  "Generate the GRAPH, and execute CALLBACK when process exits successfully.
+CALLBACK is passed the graph file as its sole argument."
+  (unless (stringp org-roam-graph-executable)
+    (user-error "`org-roam-graph-executable' is not a string"))
+  (unless (executable-find org-roam-graph-executable)
+    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
+                        "Please adjust `org-roam-graph-executable'")
+                org-roam-graph-executable))
+  (let* ((temp-dot   (make-temp-file "graph." nil ".dot" graph))
+         (temp-graph (make-temp-file "graph." nil (concat "." org-roam-graph-filetype))))
+    (org-roam-message "building graph")
+    (make-process
+     :name "*org-roam-graph*"
+     :buffer " *org-roam-graph*"
+     :command `(,org-roam-graph-executable ,temp-dot "-T" ,org-roam-graph-filetype "-o" ,temp-graph)
+     :sentinel (when callback
+                 (lambda (process _event)
+                   (when (= 0 (process-exit-status process))
+                     (progn (funcall callback temp-graph)
+                            (run-hook-with-args 'org-roam-graph-generation-hook temp-dot temp-graph))))))))
 
 (defun org-roam-graph--dot (&optional edges all-nodes)
   "Build the graphviz given the EDGES of the graph.
 If ALL-NODES, include also nodes without edges."
   (let ((org-roam-directory-temp org-roam-directory)
-        (nodes-table (org-roam--nodes-table))
+        (nodes-table (make-hash-table :test #'equal))
         (seen-nodes (list))
         (edges (or edges (org-roam-db-query [:select :distinct [source dest type] :from links]))))
+    (pcase-dolist (`(,id ,file ,title)
+                   (org-roam-db-query [:select [id file title] :from nodes]))
+      (puthash id (org-roam-node-create :file file :id id :title title) nodes-table))
     (with-temp-buffer
       (setq-local org-roam-directory org-roam-directory-temp)
       (insert "digraph \"org-roam\" {\n")
@@ -194,21 +214,63 @@ If ALL-NODES, include also nodes without edges."
       (insert "}")
       (buffer-string))))
 
+(defun org-roam-graph--connected-component (id distance)
+  "Return the edges for all nodes reachable from/connected to ID.
+DISTANCE is the maximum distance away from the root node."
+  (let* ((query
+          (if (= distance 0)
+              "
+WITH RECURSIVE
+  links_of(source, dest) AS
+  (SELECT source, dest FROM links UNION
+   SELECT dest, source FROM links),
+   connected_component(source) AS
+  (SELECT dest FROM links_of WHERE source = $s1 UNION
+   SELECT dest FROM links_of JOIN connected_component USING(source))
+SELECT DISTINCT source, dest, type FROM links
+WHERE source IN connected_component OR dest IN connected_component;"
+            "
+WITH RECURSIVE
+  links_of(source, dest) AS
+  (SELECT source, dest FROM links UNION
+   SELECT dest, source FROM links),
+  connected_component(source, trace) AS
+  (VALUES ($s1 , json_array($s1)) UNION
+   SELECT lo.dest, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.dest) FROM
+   connected_component AS cc JOIN links_of AS lo USING(source)
+   WHERE (
+    -- Avoid cycles by only visiting each node once.
+    (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.dest) == 0
+    -- Note: BFS is cut off early here.
+    AND json_array_length(cc.trace) < $s2)),
+  nodes(source) as (SELECT DISTINCT source
+   FROM connected_component GROUP BY source ORDER BY min(json_array_length(trace)))
+SELECT DISTINCT source, dest, type FROM links WHERE source IN nodes OR dest IN nodes;")))
+    (org-roam-db-query query id distance)))
+
+(defun org-roam-graph--dot-option (option &optional wrap-key wrap-val)
+  "Return dot string of form KEY=VAL for OPTION cons.
+If WRAP-KEY is non-nil it wraps the KEY.
+If WRAP-VAL is non-nil it wraps the VAL."
+  (concat wrap-key (car option) wrap-key
+          "="
+          wrap-val (cdr option) wrap-val))
+
 (defun org-roam-graph--format-node (node type)
   "Return a graphviz NODE with TYPE.
 Handles both Org-roam nodes, and string nodes (e.g. urls)."
   (let (node-id node-properties)
     (if (org-roam-node-p node)
         (let* ((title (org-roam-quote-string (org-roam-node-title node)))
-               (shortened-title (org-roam-quote-string
-                                 (pcase org-roam-graph-shorten-titles
-                                   (`truncate (org-roam-truncate org-roam-graph-max-title-length title))
-                                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
-                                   (_ title)))))
+               (shortened-title
+                (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 (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)
-                                  ("URL"     . ,(concat "org-protocol://roam-node?node="
-                                                        (url-hexify-string (org-roam-node-id node))))
+                                  ("URL"     . ,(funcall org-roam-graph-link-builder node))
                                   ("tooltip" . ,(xml-escape-string title)))))
       (setq node-id node
             node-properties (append `(("label" . ,(concat type ":" node)))
@@ -221,27 +283,6 @@ Handles both Org-roam nodes, and string nodes (e.g. urls)."
                        (append (cdr (assoc type org-roam-graph-node-extra-config))
                                node-properties) ","))))
 
-(defun org-roam-graph--build (graph &optional callback)
-  "Generate the GRAPH, and execute CALLBACK when process exits successfully.
-CALLBACK is passed the graph file as its sole argument."
-  (unless (stringp org-roam-graph-executable)
-    (user-error "`org-roam-graph-executable' is not a string"))
-  (unless (executable-find org-roam-graph-executable)
-    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
-                        "Please adjust `org-roam-graph-executable'")
-                org-roam-graph-executable))
-  (let* ((temp-dot   (make-temp-file "graph." nil ".dot" graph))
-         (temp-graph (make-temp-file "graph." nil (concat "." org-roam-graph-filetype))))
-    (org-roam-message "building graph")
-    (make-process
-     :name "*org-roam-graph--build-process*"
-     :buffer "*org-roam-graph--build-process*"
-     :command `(,org-roam-graph-executable ,temp-dot "-T" ,org-roam-graph-filetype "-o" ,temp-graph)
-     :sentinel (when callback
-                 (lambda (process _event)
-                   (when (= 0 (process-exit-status process))
-                     (funcall callback temp-graph)))))))
-
 (defun org-roam-graph--open (file)
   "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
   (pcase org-roam-graph-viewer
@@ -255,26 +296,6 @@ CALLBACK is passed the graph file as its sole argument."
     ('nil (view-file file))
     (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))
 
-;;;; Commands
-;;;###autoload
-(defun org-roam-graph (&optional arg node)
-  "Build and possibly display a graph for NODE.
-ARG may be any of the following values:
-  - nil       show the graph.
-  - `\\[universal-argument]'     show the graph for NODE.
-  - `\\[universal-argument]' N   show the graph for NODE limiting nodes to N steps."
-  (interactive
-   (list current-prefix-arg
-         (and current-prefix-arg
-              (org-roam-node-at-point 'assert))))
-  (let ((graph (cl-typecase arg
-                 (null (org-roam-graph--dot nil 'all-nodes))
-                 (cons (org-roam-graph--dot (org-roam-graph--connected-component
-                                             (org-roam-node-id node) 0)))
-                 (integer (org-roam-graph--dot (org-roam-graph--connected-component
-                                                (org-roam-node-id node) (abs arg)))))))
-    (org-roam-graph--build graph #'org-roam-graph--open)))
-
 
 (provide 'org-roam-graph)
 

extensions/org-roam-overlay.el

@@ -1,12 +1,12 @@
-;;; org-roam-overlay.el --- Link overlay for Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-
+;;; 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>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,13 +27,11 @@
 
 ;;; Commentary:
 ;;
-;; This library is an attempt at injecting Roam functionality into Org-mode.
-;; This is achieved primarily through building caches for forward links,
-;; backward links, and file titles.
-;;
+;; This extension allows to render [[id:]] links that don't have an associated
+;; descriptor with an overlay that displays the node's current title.
 ;;
 ;;; Code:
-;;;; Dependencies
+(require 'org-roam)
 
 (defface org-roam-overlay
   '((((class color) (background light))

extensions/org-roam-protocol.el

@@ -0,0 +1,193 @@
+;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 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: 2.2.0
+;; 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 extension extends `org-protocol', adding custom Org-roam handlers to it
+;; to provide the next new protocols:
+;;
+;; 1. "roam-node": This protocol simply opens the node given by the node ID
+;; 2. "roam-ref": This protocol creates or opens the node with the given REF
+;;
+;; You can find detailed instructions on how to setup the protocol in the
+;; documentation for Org-roam.
+;;
+;;; Code:
+(require 'org-protocol)
+(require 'ol) ;; for org-link-decode
+(require 'org-roam)
+
+;;; Options
+(defcustom org-roam-protocol-store-links nil
+  "Whether to store links when capturing websites with `org-roam-protocol'."
+  :type 'boolean
+  :group 'org-roam)
+
+(defcustom org-roam-capture-ref-templates
+  '(("r" "ref" plain "%?"
+     :target (file+head "${slug}.org"
+                        "#+title: ${title}")
+     :unnarrowed t))
+  "The Org-roam templates used during a capture from the roam-ref protocol.
+See `org-roam-capture-templates' for the template documentation."
+  :group 'org-roam
+  :type '(repeat
+          (choice (list :tag "Multikey description"
+                        (string :tag "Keys       ")
+                        (string :tag "Description"))
+                  (list :tag "Template entry"
+                        (string :tag "Keys           ")
+                        (string :tag "Description    ")
+                        (choice :tag "Capture Type   " :value entry
+                                (const :tag "Org entry" entry)
+                                (const :tag "Plain list item" item)
+                                (const :tag "Checkbox item" checkitem)
+                                (const :tag "Plain text" plain)
+                                (const :tag "Table line" table-line))
+                        (choice :tag "Template       "
+                                (string)
+                                (list :tag "File"
+                                      (const :format "" file)
+                                      (file :tag "Template file"))
+                                (list :tag "Function"
+                                      (const :format "" function)
+                                      (function :tag "Template function")))
+                        (plist :inline t
+                               ;; Give the most common options as checkboxes
+                               :options (((const :format "%v " :target)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
+
+;;; Handlers
+(defun org-roam-protocol-open-ref (info)
+  "Process an org-protocol://roam-ref?ref= style url with INFO.
+
+It opens or creates a note with the given ref.
+
+  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
+        encodeURIComponent(location.href) + \\='&title=\\=' + \\
+        encodeURIComponent(document.title) + \\='&body=\\=' + \\
+        encodeURIComponent(window.getSelection())"
+  (unless (plist-get info :ref)
+    (user-error "No ref key provided"))
+  (org-roam-plist-map! (lambda (k v)
+                         (org-link-decode
+                          (if (equal k :ref)
+                              (org-protocol-sanitize-uri v)
+                            v))) info)
+  (when org-roam-protocol-store-links
+    (push (list (plist-get info :ref)
+                (plist-get info :title)) org-stored-links))
+  (org-link-store-props :type (and (string-match org-link-plain-re
+                                                 (plist-get info :ref))
+                                   (match-string 1 (plist-get info :ref)))
+                        :link (plist-get info :ref)
+                        :annotation (org-link-make-string (plist-get info :ref)
+                                                          (or (plist-get info :title)
+                                                              (plist-get info :ref)))
+                        :initial (or (plist-get info :body) ""))
+  (raise-frame)
+  (let ((org-capture-link-is-already-stored t))
+    (org-roam-capture-
+     :keys (plist-get info :template)
+     :node (org-roam-node-create :title (plist-get info :title))
+     :info (list :ref (plist-get info :ref)
+                 :body (plist-get info :body))
+     :templates org-roam-capture-ref-templates))
+  nil)
+
+(defun org-roam-protocol-open-node (info)
+  "This handler simply opens the file with emacsclient.
+
+INFO is a plist containing additional information passed by the protocol URL.
+It should contain the FILE key, pointing to the path of the file to open.
+
+  Example protocol string:
+
+org-protocol://roam-node?node=uuid"
+  (when-let ((node (plist-get info :node)))
+    (raise-frame)
+    (org-roam-node-visit (org-roam-populate (org-roam-node-create :id node)) nil 'force))
+  nil)
+
+(push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
+      org-protocol-protocol-alist)
+(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

org-roam-capture.el

@@ -1,12 +1,12 @@
 ;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 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: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; 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.
 
@@ -27,42 +27,20 @@
 
 ;;; Commentary:
 ;;
-;; This library provides capture functionality for org-roam
+;; This module provides `org-capture' functionality for Org-roam. With this
+;; module the user can capture new nodes or capture new content to existing
+;; nodes.
+;;
 ;;; Code:
-;;;
-;;;; Library Requires
-(require 'org-capture)
-(eval-when-compile
-  (require 'org-roam-macs)
-  (require 'org-macs))
-(require 'org-roam-db)
-(require 'dash)
-(require 'cl-lib)
+(require 'org-roam)
 
-;; Declarations
-(declare-function org-roam-ref-add "org-roam" (ref))
-(declare-function org-datetree-find-date-create "org-datetree" (date &optional keep-restriction))
-(declare-function org-datetree-find-month-create "org-datetree" (d &optional keep-restriction))
-
-(defvar org-roam-directory)
-
-(defvar org-roam-capture--node nil
-  "The node passed during an Org-roam capture.
-This variable is populated dynamically, and is only non-nil
-during the Org-roam capture process.")
-
-(defvar org-roam-capture--info nil
-  "A property-list of additional information passed to the Org-roam template.
-This variable is populated dynamically, and is only non-nil
-during the Org-roam capture process.")
-
-(defconst org-roam-capture--template-keywords (list :if-new :id :link-description :call-location
-                                                    :region :override-default-time)
-  "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
+;;;; Declarations
+(defvar org-end-time-was-given)
 
+;;; Options
 (defcustom org-roam-capture-templates
   '(("d" "default" plain "%?"
-     :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+     :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
                         "#+title: ${title}\n")
      :unnarrowed t))
   "Templates for the creation of new entries within Org-roam.
@@ -114,30 +92,45 @@ template     The template for creating the capture item.
              in order to get a template from a file, or dynamically
              from a function.
 
-The template contains a compulsory :if-new property. This determines the
-location of the new node. The :if-new property contains a list, supporting
-the following options:
+The template contains a compulsory :target property. The :target property
+contains a list, where:
+  - The first element indicates the type of the target.
+  - The second element indicates the location of the captured node.
+  - And the rest of the list indicate the prefilled template, that will be
+    inserted and the position of the point will be adjusted for.
+    This behavior varies from type to type.
+
+The following options are supported for the :target property:
 
    (file \"path/to/file\")
        The file will be created, and prescribed an ID.
 
    (file+head \"path/to/file\" \"head content\")
        The file will be created, prescribed an ID, and head content will be
-       inserted into the file.
+       inserted if the node is a newly captured one.
 
    (file+olp \"path/to/file\" (\"h1\" \"h2\"))
-       The file will be created, prescribed an ID. The OLP (h1, h2) will be
-       created, and the point placed after.
+       The file will be created, prescribed an ID. If the file doesn't contain
+       the outline path (h1, h2), it will be automatically created. The point
+       will be adjusted to the last element in the OLP.
 
    (file+head+olp \"path/to/file\" \"head content\" (\"h1\" \"h2\"))
        The file will be created, prescribed an ID. Head content will be
-       inserted at the start of the file. The OLP (h1, h2) will be created,
-       and the point placed after.
+       inserted at the start of the file if the node is a newly captured one.
+       If the file doesn't contain the outline path (h1, h2), it will be
+       automatically created. The point will be adjusted to the last element in
+       the OLP.
 
-   (file+datetree \"path/to/file\" day)
-       The file will be created, prescribed an ID. Head content will be
-       inserted at the start of the file. The datetree will be created,
-       available options are day, week, month.
+   (file+datetree \"path/to/file\" tree-type)
+       The file will be created, prescribed an ID. A date based outline path
+       will be created for today's date. The tree-type can be one of the
+       following symbols: day, week or month. The point will adjusted to the
+       last element in the tree. To prompt for date instead of using today's,
+       use the :time-prompt property.
+
+   (node \"title or alias or ID of an existing node\")
+       The point will be placed for an existing node, based on either, its
+       title, alias or ID.
 
 The rest of the entry is a property list of additional options.  Recognized
 properties are:
@@ -212,7 +205,8 @@ be replaced with content and expanded:
               introduced with %[pathname] are expanded this way.  Since this
               happens after expanding non-interactive %-escapes, those can
               be used to fill the expression.
-  %<...>      The result of `format-time-string' on the ... format specification.
+  %<...>      The result of `format-time-string' on the ... format
+              specification.
   %t          Time stamp, date only.  The time stamp is the current time,
               except when called from agendas with `\\[org-agenda-capture]' or
               with `org-capture-use-agenda-date' set.
@@ -307,7 +301,7 @@ streamlined user experience in Org-roam."
                                       (function :tag "Template function")))
                         (plist :inline t
                                ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :if-new)
+                               :options (((const :format "%v " :target)
                                           (choice :tag "Node location"
                                                   (list :tag "File"
                                                         (const :format "" file)
@@ -342,77 +336,106 @@ streamlined user experience in Org-roam."
                                          ((const :format "%v " :table-line-pos) (string))
                                          ((const :format "%v " :kill-buffer) (const t))))))))
 
-(defvar org-roam-capture-new-node-hook (list #'org-roam-capture--insert-ref)
+(defcustom org-roam-capture-new-node-hook nil
   "Normal-mode hooks run when a new Org-roam node is created.
 The current point is the point of the new node.
-The hooks must not move the point.")
-
-(defcustom org-roam-capture-ref-templates
-  '(("r" "ref" plain "%?"
-     :if-new (file+head "${slug}.org"
-                        "#+title: ${title}")
-     :unnarrowed t))
-  "The Org-roam templates used during a capture from the roam-ref protocol.
-See `org-roam-capture-templates' for the template documentation."
+The hooks must not move the point."
   :group 'org-roam
-  :type '(repeat
-          (choice (list :tag "Multikey description"
-                        (string :tag "Keys       ")
-                        (string :tag "Description"))
-                  (list :tag "Template entry"
-                        (string :tag "Keys           ")
-                        (string :tag "Description    ")
-                        (choice :tag "Capture Type   " :value entry
-                                (const :tag "Org entry" entry)
-                                (const :tag "Plain list item" item)
-                                (const :tag "Checkbox item" checkitem)
-                                (const :tag "Plain text" plain)
-                                (const :tag "Table line" table-line))
-                        (choice :tag "Template       "
-                                (string)
-                                (list :tag "File"
-                                      (const :format "" file)
-                                      (file :tag "Template file"))
-                                (list :tag "Function"
-                                      (const :format "" function)
-                                      (function :tag "Template function")))
-                        (plist :inline t
-                               ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :if-new)
-                                          (choice :tag "Node location"
-                                                  (list :tag "File"
-                                                        (const :format "" file)
-                                                        (string :tag "  File"))
-                                                  (list :tag "File & Head Content"
-                                                        (const :format "" file+head)
-                                                        (string :tag "  File")
-                                                        (string :tag "  Head Content"))
-                                                  (list :tag "File & Outline path"
-                                                        (const :format "" file+olp)
-                                                        (string :tag "  File")
-                                                        (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))
-                                                  (list :tag "File & Head Content & Outline path"
-                                                        (const :format "" file+head+olp)
-                                                        (string :tag "  File")
-                                                        (string :tag "  Head Content")
-                                                        (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))))
-                                         ((const :format "%v " :prepend) (const t))
-                                         ((const :format "%v " :immediate-finish) (const t))
-                                         ((const :format "%v " :jump-to-captured) (const t))
-                                         ((const :format "%v " :empty-lines) (const 1))
-                                         ((const :format "%v " :empty-lines-before) (const 1))
-                                         ((const :format "%v " :empty-lines-after) (const 1))
-                                         ((const :format "%v " :clock-in) (const t))
-                                         ((const :format "%v " :clock-keep) (const t))
-                                         ((const :format "%v " :clock-resume) (const t))
-                                         ((const :format "%v " :time-prompt) (const t))
-                                         ((const :format "%v " :tree-type) (const week))
-                                         ((const :format "%v " :unnarrowed) (const t))
-                                         ((const :format "%v " :table-line-pos) (string))
-                                         ((const :format "%v " :kill-buffer) (const t))))))))
+  :type 'hook)
 
+(defvar org-roam-capture-preface-hook nil
+  "Hook run when Org-roam tries to determine capture location of the node.
+If any hook returns a value (which should be an ID), all hooks
+after it are ignored.
+
+With this hook you can hijack controls over the location of the
+node for which the capture process is currently running for, or
+use to just perform an arbitrary side effect, e.g. modify the
+state related to the capture process. See `org-roam-protocol' and
+`org-roam-dailies' as examples for what and how this hook is used
+for.
+
+If you're trying to perform the hijack, it's mandatory for you to:
+  1. Set the currently active buffer for editing operations using
+     `org-capture-target-buffer'.
+  2. Place the point in this buffer from where the location starts
+     from (e.g. if it's a file based node it should be the BOB,
+     otherwise it should be the position from where the heading
+     based node starts from).
+  3. Return the ID (as a string) of the capturing node.
+
+If you use this hook for any other purpose, but not the hijack,
+it's mandatory that you should return nil as the return value; so
+the capture process would be able to setup the capture buffer.
+
+If you need to do something when you capture new nodes, use
+`org-roam-capture-new-node-hook' instead of this hook.
+
+WARNING: This hook is primarily designed for the usage by the
+extensions and packages, and requires understanding of the
+internal capture process. If you don't understand it, you should
+learn these internals before using this or use it at your own
+risk breaking things.")
+
+;;; Variables
+
+(defvar org-roam-capture--node nil
+  "The node passed during an Org-roam capture.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defvar org-roam-capture--info nil
+  "A property-list of additional information passed to the Org-roam template.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defconst org-roam-capture--template-keywords (list :target :id :link-description :call-location
+                                                    :region)
+  "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
+
+;;; Main entry point
+;;;###autoload
+(cl-defun org-roam-capture- (&key goto keys node info props templates)
+  "Main entry point of `org-roam-capture' module.
+GOTO and KEYS correspond to `org-capture' arguments.
+INFO is a plist for filling up Org-roam's capture templates.
+NODE is an `org-roam-node' construct containing information about the node.
+PROPS is a plist containing additional Org-roam properties for each template.
+TEMPLATES is a list of org-roam templates."
+  (let* ((props (plist-put props :call-location (point-marker)))
+         (org-capture-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)
+               (= (length org-capture-templates) 1))
+      (setq keys (caar org-capture-templates)))
+    (org-capture goto keys)))
+
+;;;###autoload
+(cl-defun org-roam-capture (&optional goto keys &key filter-fn templates info)
+  "Launches an `org-capture' process for a new or existing node.
+This uses the templates defined at `org-roam-capture-templates'.
+Arguments GOTO and KEYS see `org-capture'.
+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.
+The TEMPLATES, if provided, override the list of capture templates (see
+`org-roam-capture-'.)
+The INFO, if provided, is passed along to the underlying `org-roam-capture-'."
+  (interactive "P")
+  (let ((node (org-roam-node-read nil filter-fn)))
+    (org-roam-capture- :goto goto
+                       :info info
+                       :keys keys
+                       :templates templates
+                       :node node
+                       :props '(:immediate-finish nil))))
+
+;;; Capture process
 (defun org-roam-capture-p ()
   "Return t if the current capture process is an Org-roam capture.
 This function is to only be called when `org-capture-plist' is
@@ -424,159 +447,81 @@ the capture)."
   "Get the value for KEYWORD from the `org-roam-capture-template'."
   (plist-get (plist-get org-capture-plist :org-roam) keyword))
 
-(defun org-roam-capture--put (&rest stuff)
-  "Put properties from STUFF into the `org-roam-capture-template'."
+(defun org-roam-capture--put (prop value)
+  "Set property PROP to VALUE in the `org-roam-capture-template'."
   (let ((p (plist-get org-capture-plist :org-roam)))
-    (while stuff
-      (setq p (plist-put p (pop stuff) (pop stuff))))
     (setq org-capture-plist
-          (plist-put org-capture-plist :org-roam p))))
+          (plist-put org-capture-plist
+                     :org-roam
+                     (plist-put p prop value)))))
 
-;; FIXME: Pending upstream patch
-;; https://orgmode.org/list/87h7tv9pkm.fsf@hidden/T/#u
-;;
-;; Org-capture's behaviour right now is that `org-capture-plist' is valid only
-;; during the initialization of the Org-capture buffer. The value of
-;; `org-capture-plist' is saved into buffer-local `org-capture-current-plist'.
-;; However, the value for that particular capture is no longer accessible for
-;; hooks in `org-capture-after-finalize-hook', since the capture buffer has been
-;; cleaned up.
-;;
-;; This advice restores the global `org-capture-plist' during finalization, so
-;; the plist is valid during both initialization and finalization of the
-;; capture.
-(defun org-roam-capture--update-plist (&optional _)
-  "Update global plist from local var."
-  (setq org-capture-plist org-capture-current-plist))
+;;;; Capture target
+(defun org-roam-capture--prepare-buffer ()
+  "Prepare the capture buffer for the current Org-roam based capture template.
+This function will initialize and setup the capture buffer,
+position the point to the current :target (and if necessary,
+create it if it doesn't exist), and place the point for further
+processing by `org-capture'.
 
-(advice-add 'org-capture-finalize :before #'org-roam-capture--update-plist)
+Note: During the capture process this function is run by
+`org-capture-set-target-location', as a (function ...) based
+capture target."
+  (if-let ((id (run-hook-with-args-until-success 'org-roam-capture-preface-hook)))
+      (org-roam-capture--put :id id)
+    (org-roam-capture--setup-target-location))
+  (let ((template (org-capture-get :template)))
+    (when (stringp template)
+      (org-capture-put
+       :template
+       (org-roam-capture--fill-template template))))
+  (org-roam-capture--put :finalize (or (org-capture-get :finalize)
+                                       (org-roam-capture--get :finalize))))
 
-(defun org-roam-capture--finalize-find-file ()
-  "Visit the buffer after Org-capture is done.
-This function is to be called in the Org-capture finalization process.
-ID is unused."
-  (switch-to-buffer (org-capture-get :buffer)))
-
-(defun org-roam-capture--finalize-insert-link ()
-  "Insert a link to ID into the buffer where Org-capture was called.
-ID is the Org id of the newly captured content.
-This function is to be called in the Org-capture finalization process."
-  (when-let* ((mkr (org-roam-capture--get :call-location))
-              (buf (marker-buffer mkr)))
-    (with-current-buffer buf
-      (when-let ((region (org-roam-capture--get :region)))
-        (org-roam-unshield-region (car region) (cdr region))
-        (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)))))))
-
-(defun org-roam-capture--finalize ()
-  "Finalize the `org-roam-capture' process."
-  (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 (find-buffer-visiting new-file)
-          (kill-buffer (find-buffer-visiting new-file)))
-        (delete-file new-file))
-    (when-let* ((finalize (org-roam-capture--get :finalize))
-                (org-roam-finalize-fn (intern (concat "org-roam-capture--finalize-"
-                                                      (symbol-name finalize)))))
-      (if (functionp org-roam-finalize-fn)
-          (funcall org-roam-finalize-fn)
-        (funcall finalize))))
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize))
-
-(defun org-roam-capture--install-finalize ()
-  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
-  (when (org-roam-capture-p)
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
-
-(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize)
-
-(defun org-roam-capture--fill-template (template &optional org-capture-p)
-  "Expand TEMPLATE and return it.
-It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
-also run Org-capture's template expansion."
-  (funcall (if org-capture-p #'org-capture-fill-template #'identity)
-           (org-roam-format
-            template
-            (lambda (key)
-              (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 (completing-read (format "%s: " key) nil)))
-                      (plist-put org-roam-capture--info ksym r)
-                      r))))))))
-
-(defun org-roam-capture--insert-ref ()
-  "Insert the ref if any."
-  (when-let ((ref (plist-get org-roam-capture--info :ref)))
-    (org-roam-ref-add ref)))
-
-(defun org-roam-capture--goto-location ()
-  "Initialize the buffer, and goto the location of the new capture.
-Return the ID of the location."
-  (let (p)
-    (pcase (or (org-roam-capture--get :if-new)
-               (user-error "Template needs to specify `:if-new'"))
+(defun org-roam-capture--setup-target-location ()
+  "Initialize the buffer, and goto the location of the new capture."
+  (let ((target-entry-p t)
+        p new-file-p id)
+    (pcase (org-roam-capture--get-target)
       (`(file ,path)
-       (setq path (expand-file-name
-                   (string-trim (org-roam-capture--fill-template path t))
-                   org-roam-directory))
-       (unless (file-exists-p path)
-         (org-roam-capture--put :new-file path))
+       (setq path (org-roam-capture--target-truepath path)
+             new-file-p (org-roam-capture--new-file-p path))
+       (when new-file-p (org-roam-capture--put :new-file path))
        (set-buffer (org-capture-target-buffer path))
        (widen)
-       (setq p (goto-char (point-min))))
+       (setq p (goto-char (point-min))
+             target-entry-p nil))
       (`(file+olp ,path ,olp)
-       (setq path (expand-file-name
-                   (string-trim (org-roam-capture--fill-template path t))
-                   org-roam-directory))
+       (setq path (org-roam-capture--target-truepath path)
+             new-file-p (org-roam-capture--new-file-p path))
+       (when new-file-p (org-roam-capture--put :new-file path))
        (set-buffer (org-capture-target-buffer path))
-       (unless (file-exists-p path)
-         (org-roam-capture--put :new-file path))
        (setq p (point-min))
        (let ((m (org-roam-capture-find-or-create-olp olp)))
          (goto-char m))
        (widen))
       (`(file+head ,path ,head)
-       (setq path (expand-file-name
-                   (string-trim (org-roam-capture--fill-template path t))
-                   org-roam-directory))
+       (setq path (org-roam-capture--target-truepath path)
+             new-file-p (org-roam-capture--new-file-p path))
        (set-buffer (org-capture-target-buffer path))
-       (unless (file-exists-p path)
+       (when new-file-p
          (org-roam-capture--put :new-file path)
          (insert (org-roam-capture--fill-template head t)))
        (widen)
-       (setq p (goto-char (point-min))))
+       (setq p (goto-char (point-min))
+             target-entry-p nil))
       (`(file+head+olp ,path ,head ,olp)
-       (setq path (expand-file-name
-                   (string-trim (org-roam-capture--fill-template path t))
-                   org-roam-directory))
-       (widen)
+       (setq path (org-roam-capture--target-truepath path)
+             new-file-p (org-roam-capture--new-file-p path))
        (set-buffer (org-capture-target-buffer path))
-       (unless (file-exists-p path)
+       (widen)
+       (when new-file-p
          (org-roam-capture--put :new-file path)
          (insert (org-roam-capture--fill-template head t)))
        (setq p (point-min))
        (let ((m (org-roam-capture-find-or-create-olp olp)))
          (goto-char m)))
       (`(file+datetree ,path ,tree-type)
-       (setq path (expand-file-name
-                   (string-trim (org-roam-capture--fill-template path t))
-                   org-roam-directory))
+       (setq path (org-roam-capture--target-truepath path))
        (require 'org-datetree)
        (widen)
        (set-buffer (org-capture-target-buffer path))
@@ -622,55 +567,68 @@ Return the ID of the location."
        ;; first try to get ID, then try to get title/alias
        (let ((node (or (org-roam-node-from-id title-or-id)
                        (org-roam-node-from-title-or-alias title-or-id)
-                       (user-error "No node with title or id \"%s\" title-or-id"))))
+                       (user-error "No node with title or id \"%s\"" title-or-id))))
          (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
          (goto-char (org-roam-node-point node))
-         (setq p (org-roam-node-point node)))))
-    (prog1
-        ;; Setup `org-id' for the current capture target and return it back to
-        ;; the 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))
-          (prog1
-              (org-id-get-create)
-            (run-hooks 'org-roam-capture-new-node-hook)))
-      ;; Adjust the point only after ID was generated and polluted to the
-      ;; current target in the capture buffer.
-      (org-roam-capture--adjust-point-for-capture-type))))
-
-(defun org-roam-capture--adjust-point-for-capture-type (&optional pos)
-  "Reposition the point for template insertion dependently on the capture type.
-Return the newly adjusted position of `point'.
-
-POS is the current position of point (an integer) inside the
-currently active capture buffer, where the adjustment should
-start to begin from. If it's nil, then it will default to
-the current value of `point'."
-  (or pos (setq pos (point)))
-  (goto-char pos)
-  (let ((location-type (if (= pos 1) 'beginning-of-file 'heading-at-point)))
-    (and (eq location-type 'heading-at-point)
-         (cl-assert (org-at-heading-p)))
+         (setq p (org-roam-node-point node)
+               target-entry-p (and (derived-mode-p 'org-mode) (org-at-heading-p))))))
+    ;; Setup `org-id' for the current capture target and return it back to the
+    ;; caller.
+    ;; Unless it's an entry type, then we want to create an ID for the entry instead
     (pcase (org-capture-get :type)
-      (`plain
-       (cl-case location-type
-         (beginning-of-file
-          (if (org-capture-get :prepend)
-              (let ((el (org-element-at-point)))
-                (while (and (not (eobp))
-                            (memq (org-element-type el)
-                                  '(drawer property-drawer keyword comment comment-block horizontal-rule)))
-                  (goto-char (org-element-property :end el))
-                  (setq el (org-element-at-point))))
-            (goto-char (org-entry-end-position))))
-         (heading-at-point
-          (if (org-capture-get :prepend)
-              (org-end-of-meta-data t)
-            (goto-char (org-entry-end-position))))))))
-  (point))
+      ('entry
+       (advice-add #'org-capture-place-entry :after #'org-roam-capture--create-id-for-entry)
+       (org-roam-capture--put :new-node-p t)
+       (setq id (org-roam-node-id org-roam-capture--node)))
+      (_
+       (save-excursion
+         (goto-char p)
+         (unless (org-entry-get p "ID")
+           (org-roam-capture--put :new-node-p t))
+         (setq id (or (org-entry-get p "ID")
+                      (org-roam-node-id org-roam-capture--node)))
+         (setf (org-roam-node-id org-roam-capture--node) id)
+         (org-entry-put p "ID" id))))
+    (org-roam-capture--put :id id)
+    (org-roam-capture--put :target-entry-p target-entry-p)
+    (advice-add #'org-capture-place-template :before #'org-roam-capture--set-target-entry-p-a)
+    (advice-add #'org-capture-place-template :after #'org-roam-capture-run-new-node-hook-a)))
+
+(defun org-roam-capture--set-target-entry-p-a (_)
+  "Correct `:target-entry-p' in Org-capture template based on `:target.'"
+  (org-capture-put :target-entry-p (org-roam-capture--get :target-entry-p))
+  (advice-remove #'org-capture-place-template #'org-roam-capture--set-target-entry-p-a))
+
+(defun org-roam-capture-run-new-node-hook-a (_)
+  "Advice to run after the Org-capture template is placed."
+  (when (org-roam-capture--get :new-node-p)
+    (run-hooks 'org-roam-capture-new-node-hook))
+  (advice-remove #'org-capture-place-template #'org-roam-capture--place-template-a))
+
+(defun org-roam-capture--create-id-for-entry ()
+  "Create the ID for the new entry."
+  (org-entry-put (point) "ID" (org-roam-capture--get :id))
+  (advice-remove #'org-capture-place-entry #'org-roam-capture--create-id-for-entry))
+
+(defun org-roam-capture--get-target ()
+  "Get the current capture :target for the capture template in use."
+  (or (org-roam-capture--get :target)
+      (user-error "Template needs to specify `:target'")))
+
+(defun org-roam-capture--target-truepath (path)
+  "From PATH get the correct path to the current capture target and return it.
+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)
+                    (string-trim)
+                    (expand-file-name org-roam-directory))))
+
+(defun org-roam-capture--new-file-p (path)
+  "Return t if PATH is for a new file with no visiting buffer."
+  (not (or (file-exists-p path)
+           (org-find-base-buffer-visiting path))))
 
 (defun org-roam-capture-find-or-create-olp (olp)
   "Return a marker pointing to the entry at OLP in the current buffer.
@@ -688,6 +646,7 @@ 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))
        (let ((re (format org-complex-heading-regexp-format
                          (regexp-quote heading)))
              (cnt 0))
@@ -718,52 +677,91 @@ you can catch it with `condition-case'."
              end (save-excursion (org-end-of-subtree t t))))
      (point-marker))))
 
-(defun org-roam-capture--get-node-from-ref (ref)
-  "Return the node from reference REF."
-  (save-match-data
-    (when (string-match org-link-plain-re ref)
-      (let ((type (match-string 1 ref))
-            (path (match-string 2 ref)))
-        (when-let ((id (caar (org-roam-db-query
-                              [:select [nodes:id]
-                               :from refs
-                               :left-join nodes
-                               :on (= refs:node-id nodes:id)
-                               :where (= refs:type $s1)
-                               :and (= refs:ref $s2)
-                               :limit 1]
-                              type path))))
-          (org-roam-populate (org-roam-node-create :id id)))))))
+;;;; Finalizers
+(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize-h)
+(defun org-roam-capture--install-finalize-h ()
+  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
+  (when (org-roam-capture-p)
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
 
-(defun org-roam-capture--get-point ()
-  "Return exact point to file for org-capture-template.
-This function is used solely in Org-roam's capture templates: see
-`org-roam-capture-templates'."
-  (when (org-roam-capture--get :override-default-time)
-    (org-capture-put :default-time (org-roam-capture--get :override-default-time)))
-  (let ((id (cond ((plist-get org-roam-capture--info :ref)
-                   (if-let ((node (org-roam-capture--get-node-from-ref
-                                   (plist-get org-roam-capture--info :ref))))
-                       (progn
-                         (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
-                         (goto-char (org-roam-node-point node))
-                         (widen)
-                         (org-end-of-subtree t t))
-                     (org-roam-capture--goto-location)))
-                  ((and (org-roam-node-file org-roam-capture--node)
-                        (org-roam-node-point org-roam-capture--node))
-                   (set-buffer (org-capture-target-buffer (org-roam-node-file org-roam-capture--node)))
-                   (goto-char (org-roam-node-point org-roam-capture--node))
-                   (widen)
-                   (org-end-of-subtree t t)
-                   (org-roam-node-id org-roam-capture--node))
-                  (t
-                   (org-roam-capture--goto-location)))))
-    (org-capture-put :template
-                     (org-roam-capture--fill-template (org-capture-get :template)))
-    (org-roam-capture--put :id id)
-    (org-roam-capture--put :finalize (or (org-capture-get :finalize)
-                                         (org-roam-capture--get :finalize)))))
+(defun org-roam-capture--finalize ()
+  "Finalize the `org-roam-capture' process."
+  (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 (find-buffer-visiting new-file)
+          (kill-buffer (find-buffer-visiting new-file)))
+        (delete-file new-file))
+    (when-let* ((finalize (org-roam-capture--get :finalize))
+                (org-roam-finalize-fn (intern (concat "org-roam-capture--finalize-"
+                                                      (symbol-name finalize)))))
+      (if (functionp org-roam-finalize-fn)
+          (funcall org-roam-finalize-fn)
+        (funcall finalize))))
+  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize))
+
+(defun org-roam-capture--finalize-find-file ()
+  "Visit the buffer after Org-capture is done.
+This function is to be called in the Org-capture finalization process.
+ID is unused."
+  (switch-to-buffer (org-capture-get :buffer)))
+
+(defun org-roam-capture--finalize-insert-link ()
+  "Insert a link to ID into the buffer where Org-capture was called.
+ID is the Org id of the newly captured content.
+This function is to be called in the Org-capture finalization process."
+  (when-let* ((mkr (org-roam-capture--get :call-location))
+              (buf (marker-buffer mkr)))
+    (with-current-buffer buf
+      (when-let ((region (org-roam-capture--get :region)))
+        (org-roam-unshield-region (car region) (cdr region))
+        (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)))))))
+
+;;;; Processing of the capture templates
+(defun org-roam-capture--fill-template (template &optional org-capture-p newline)
+  "Expand TEMPLATE and return it.
+It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
+also run Org-capture's template expansion.
+If NEWLINE, ensure that the template returned ends with a newline."
+  (setq template (org-roam-format-template
+                  template
+                  (lambda (key default-val)
+                    (let ((fn (intern key))
+                          (node-fn (intern (concat "org-roam-node-" key)))
+                          (ksym (intern (concat ":" key))))
+                      (cond
+                       ((fboundp fn)
+                        (funcall fn org-roam-capture--node))
+                       ((fboundp node-fn)
+                        (funcall node-fn org-roam-capture--node))
+                       ((plist-get org-roam-capture--info ksym)
+                        (plist-get org-roam-capture--info ksym))
+                       (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
+                            (plist-put org-roam-capture--info ksym r)
+                            r)))))))
+  ;; WARNING:
+  ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
+  ;; template does not start with any whitespace, and only ends with a single newline
+  ;;
+  ;; In most cases where we rely on `org-capture-fill-template' to populate non-org-capture-related templates,
+  ;; (e.g. in OLPs), we strip the final newline, obtaining a template that seems to be string-trimmed.
+  ;;
+  ;; This means that if the original passed template has newlines, and ORG-CAPTURE-P is true, then the extra
+  ;; whitespace specified in the template will be ignored.
+  (when org-capture-p
+    (setq template
+          (replace-regexp-in-string "\n$" "" (org-capture-fill-template template))))
+  (when (and newline
+             (not (string-suffix-p "\n" template)))
+    (setq template (concat template "\n")))
+  template)
 
 (defun org-roam-capture--convert-template (template &optional props)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax.
@@ -772,7 +770,9 @@ properties to be added to the template."
   (pcase template
     (`(,_key ,_desc)
      template)
-    (`(,key ,desc ,type ,body . ,rest)
+    ((or `(,key ,desc ,type ignore ,body . ,rest)
+         `(,key ,desc ,type (function ignore) ,body . ,rest)
+         `(,key ,desc ,type ,body . ,rest))
      (setq rest (append rest props))
      (let (org-roam-plist options)
        (while rest
@@ -785,43 +785,12 @@ properties to be added to the template."
            (if custom
                (setq org-roam-plist (plist-put org-roam-plist key val))
              (setq options (plist-put options key val)))))
-       (append `(,key ,desc ,type #'org-roam-capture--get-point ,body)
+       (append `(,key ,desc ,type #'org-roam-capture--prepare-buffer ,body)
                options
                (list :org-roam org-roam-plist))))
     (_
      (signal 'invalid-template template))))
 
-;;;###autoload
-(cl-defun org-roam-capture- (&key goto keys node info props templates)
-  "Main entry point.
-GOTO and KEYS correspond to `org-capture' arguments.
-INFO is an alist for filling up Org-roam's capture templates.
-NODE is an `org-roam-node' construct containing information about the node.
-PROPS is a plist containing additional Org-roam properties for each template.
-TEMPLATES is a list of org-roam templates."
-  (let* ((props (plist-put props :call-location (point-marker)))
-         (org-capture-templates
-          (mapcar (lambda (template)
-                    (org-roam-capture--convert-template template props))
-                  (or templates org-roam-capture-templates)))
-         (org-roam-capture--node node)
-         (org-roam-capture--info info))
-    (when (and (not keys)
-               (= (length org-capture-templates) 1))
-      (setq keys (caar org-capture-templates)))
-    (org-capture goto keys)))
-
-;;;###autoload
-(defun org-roam-capture (&optional goto keys)
-  "Launches an `org-capture' process for a new or existing note.
-This uses the templates defined at `org-roam-capture-templates'.
-Arguments GOTO and KEYS see `org-capture'."
-  (interactive "P")
-  (let ((node (org-roam-node-read)))
-    (org-roam-capture- :goto goto
-                       :keys keys
-                       :node node
-                       :props '(:immediate-finish nil))))
 
 (provide 'org-roam-capture)
 

org-roam-compat.el

@@ -1,12 +1,12 @@
-;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-roam-compat.el --- Backward compatibility code -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 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: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; Package-Requires: ((emacs "26.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,11 +27,11 @@
 
 ;;; Commentary:
 ;;
-;; This file contains code needed for backward compatibility with older Emacsen
-;; and previous versions of org-roam.
+;; This file is dedicated to maintain backward compatibility with older older
+;; Emacsen and Org-roam versions.
 ;;
 ;;; Code:
-;;;; Library Requires
+(require 'org-roam)
 
 ;;; Backports
 ;; REVIEW Remove when 26.x support is dropped. This is exact the same as
@@ -97,7 +97,111 @@ recursion."
             (push (concat dir "/" file) files)))))
     (nconc result (nreverse files))))
 
+;;; Compatibility hacks and patches
+(advice-add #'org-id-add-location :around #'org-roam--handle-absent-org-id-locations-file-a)
+(defun org-roam--handle-absent-org-id-locations-file-a (fn &rest args)
+  "Gracefully handle errors related to absence of `org-id-locations-file'.
+FN is `org-id-add-location' that comes from advice and ARGS are
+passed to it."
+  (condition-case err
+      (apply fn args)
+    ;; `org-id' makes the assumption that `org-id-locations-file' will be stored in `user-emacs-directory'
+    ;; which always exist if you have Emacs, so it uses `with-temp-file' to write to the file. However, the
+    ;; users *do* change the path to this file and `with-temp-file' unable to create the file, if the path to
+    ;; it consists of directories that don't exist. We'll have to handle this ourselves.
+    (error
+     (advice-remove 'org-id-add-location #'org-roam--handle-absent-org-id-locations-file-a)
+     (if (file-exists-p (file-truename org-id-locations-file))
+         (signal (car err) (cdr err))
+       ;; Pre-allocate the hash table to avoid weird access related errors during the regeneration.
+       (or org-id-locations (setq org-id-locations (make-hash-table :test 'equal)))
+       ;; If permissions allow that, try to create the user specified directory path to
+       ;; `org-id-locations-file' ourselves.
+       (condition-case _err
+           (progn (org-roam-message (concat "`org-id-locations-file' (%s) doesn't exist. "
+                                            "Trying to regenerate it (this may take a while)...")
+                                    org-id-locations-file)
+                  (make-directory (file-name-directory (file-truename org-id-locations-file)))
+                  (org-roam-update-org-id-locations)
+                  (apply fn args))
+         ;; In case of failure (lack of permissions), we'll patch it to at least handle the current session
+         ;; without errors.
+         (file-error (org-roam-message "Failed to regenerate `org-id-locations-file'")
+                     (lwarn 'org-roam :error "
+--------
+WARNING: `org-id-locations-file' (%s) doesn't exist!
+         Org-roam is unable to create it for you.
+--------
+
+This happens when Emacs doesn't have permissions to create the
+path to your `org-id-locations-file'. Org-roam will now fallback
+storing the file in your current `org-roam-directory', but the
+warning will keep popup with each new session.
+
+To stop this warning from popping up, set `org-id-locations-file'
+to the location you want and ensure that the path exists on your
+filesystem, then run M-x `org-roam-update-org-id-locations'.
+
+Note: While Org-roam doesn't depend on `org-id-locations-file' to
+lookup IDs for the nodes that are stored in the database, it
+still tries to keep it updated so IDs work across other files in
+Org-mode, so the IDs used in your `org-roam-directory' would be
+able to cross-reference outside of `org-roam-directory'. It also
+allows to keep linking with \"id:\" links within the current
+`org-roam-directory' to headings and files that are excluded from
+identification (e.g. with \"ROAM_EXCLUDE\" property) as Org-roam
+nodes." org-id-locations-file)
+                     (setq org-id-locations-file
+                           (expand-file-name ".orgids" (file-truename org-roam-directory)))
+                     (apply fn args)))))))
+
+;;;; Deprecated :if-new capture template keyword
+(with-eval-after-load 'org-roam-capture
+  (add-to-list 'org-roam-capture--template-keywords :if-new)
+
+  (let ((inhibit-warning-p t)) ; REVIEW Set this to nil close to next major release
+    (advice-add 'org-roam-capture--get-target :around #'org-roam-capture--get-if-new-target-a)
+    (defun org-roam-capture--get-if-new-target-a (fn &rest args)
+      "Get the current capture target using deprecated :if-new property."
+      (if-let ((target (org-roam-capture--get :if-new)))
+          (prog1 target
+            (unless inhibit-warning-p
+              (lwarn 'org-roam-capture :warning
+                     (mapconcat
+                      #'identity
+                      ["`:if-new' property is deprecated in favor of `:target'."
+                       "This warning will popup once per each session. In order to get"
+                       "rid of it, rename all the references to the `:if-new' property"
+                       "in your capture templates to `:target'."]
+                      "\n"))
+              ;; Don't irritate the user too much. Displaying the warning once per session should be enough.
+              (setq inhibit-warning-p t)))
+        (apply fn args)))))
+
 ;;; Obsolete aliases (remove after next major release)
+(define-obsolete-function-alias
+  'org-roam-setup
+  'org-roam-db-autosync-enable "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-teardown
+  'org-roam-db-autosync-disable "org-roam 2.0")
+
+(define-obsolete-variable-alias
+  'org-roam-current-node
+  'org-roam-buffer-current-node "org-roam 2.0")
+(define-obsolete-variable-alias
+  'org-roam-current-directory
+  'org-roam-buffer-current-directory "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-buffer-render
+  'org-roam-buffer-render-contents "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-buffer
+  'org-roam-buffer-display-dedicated "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-visit-thing
+  'org-roam-buffer-visit-thing "org-roam 2.0")
+
 (define-obsolete-function-alias
   'org-roam-dailies-find-today
   'org-roam-dailies-goto-today "org-roam 2.0")
@@ -117,7 +221,16 @@ recursion."
   'org-roam-dailies-find-date
   'org-roam-dailies-goto-date "org-roam 2.0")
 
+(define-obsolete-function-alias
+  'org-roam-add-property
+  'org-roam-property-add "org-roam 2.1")
+
+(define-obsolete-function-alias
+  'org-roam-remove-property
+  'org-roam-property-remove "org-roam 2.1")
+
 ;;; Obsolete functions
+(make-obsolete 'org-roam-get-keyword 'org-collect-keywords "org-roam 2.0")
 
 (provide 'org-roam-compat)
 

org-roam-completion.el

@@ -1,107 +0,0 @@
-;;; org-roam-completion.el --- Completion features -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 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: 2.0.0
-;; 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 "2.90.1"))
-;; 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 library provides completion-at-point functions for Org-roam.
-;;
-;; The two main functions provided to capf are:
-;;
-;;    `org-roam-complete-link-at-point' provides completions to nodes
-;;    within link brackets
-;;
-;;    `org-roam-complete-everywhere' provides completions for nodes everywhere,
-;;    matching the symbol at point
-;;
-;;; Code:
-(require 'cl-lib)
-(require 'org-element)
-
-(declare-function org-roam--get-titles "org-roam")
-
-(defcustom org-roam-completion-everywhere nil
-  "When non-nil, provide link completion matching outside of Org links."
-  :group 'org-roam
-  :type 'boolean)
-
-(defvar org-roam-completion-functions (list #'org-roam-complete-link-at-point
-                                            #'org-roam-complete-everywhere)
-  "List of functions to be used with `completion-at-point' for Org-roam.")
-
-(defconst org-roam-bracket-completion-re
-  "\\[\\[\\(\\(?:roam:\\)?\\)\\([^z-a]*\\)]]"
-  "Regex for completion within link brackets.
-We use this as a substitute for `org-link-bracket-re', because
-`org-link-bracket-re' requires content within the brackets for a match.")
-
-(defun org-roam-complete-everywhere ()
-  "Provides completions for links for any word at point.
-This is a `completion-at-point' function, and is active when
-`org-roam-completion-everywhere' is non-nil."
-  (when (and org-roam-completion-everywhere
-             (thing-at-point 'word)
-             (not (save-match-data (org-in-regexp org-link-any-re))))
-    (let ((bounds (bounds-of-thing-at-point 'word)))
-      (list (car bounds) (cdr bounds)
-            (completion-table-dynamic
-             (lambda (_)
-               (funcall #'org-roam--get-titles)))
-            :exit-function
-            (lambda (str _status)
-              (delete-char (- (length str)))
-              (insert "[[roam:" str "]]"))))))
-
-(defun org-roam-complete-link-at-point ()
-  "Do appropriate completion for the link at point."
-  (let (roam-p start end)
-    (when (org-in-regexp org-roam-bracket-completion-re 1)
-      (setq roam-p (not (string-blank-p (match-string 1)))
-            start (match-beginning 2)
-            end (match-end 2))
-      (list start end
-            (completion-table-dynamic
-             (lambda (_)
-               (funcall #'org-roam--get-titles)))
-            :exit-function
-            (lambda (str &rest _)
-              (delete-char (- 0 (length str)))
-              (insert (concat (unless roam-p "roam:")
-                              str))
-              (forward-char 2))))))
-
-(defun org-roam-complete-at-point ()
-  "."
-  (run-hook-with-args-until-success 'org-roam-completion-functions))
-
-(defun org-roam--register-completion-functions ()
-  "."
-  (add-hook 'completion-at-point-functions #'org-roam-complete-at-point nil t))
-
-(add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions)
-
-(provide 'org-roam-completion)
-
-;;; org-roam-completion.el ends here

org-roam-db.el

@@ -1,12 +1,12 @@
 ;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 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: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; 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.
 
@@ -27,36 +27,35 @@
 
 ;;; Commentary:
 ;;
-;; This library provides the underlying database api to org-roam.
+;; This module provides the underlying database API to Org-roam.
 ;;
 ;;; Code:
-;;;; Library Requires
-(eval-when-compile (require 'subr-x))
-(require 'emacsql)
-(require 'emacsql-sqlite)
-(require 'seq)
+(require 'org-roam)
+(defvar org-outline-path-cache)
 
-(eval-and-compile
-  (require 'org-roam-macs)
-  ;; For `org-with-wide-buffer'
-  (require 'org-macs))
-(require 'org)
-(require 'ol)
-(require 'org-roam-utils)
+;;; 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
+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
+  :type '(choice (const sqlite)
+                 (const libsqlite3)
+                 (const sqlite3)
+                 (symbol :tag "other")))
 
-(defvar org-roam-find-file-hook)
-(defvar org-roam-directory)
-(defvar org-roam-verbose)
-(defvar org-agenda-files)
-
-(declare-function org-roam-id-at-point "org-roam")
-(declare-function org-roam--list-all-files "org-roam")
-(declare-function org-roam-node-at-point "org-roam")
-
-;;;; Options
-(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
-  "The full path to file where the Org-roam database is stored.
-If this is non-nil, the Org-roam sqlite database is saved here.
+(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
 when used with multiple Org-roam instances."
@@ -65,40 +64,98 @@ when used with multiple Org-roam instances."
 
 (defcustom org-roam-db-gc-threshold gc-cons-threshold
   "The value to temporarily set the `gc-cons-threshold' threshold to.
-During large, heavy operations like `org-roam-db-sync',
-many GC operations happen because of the large number of
-temporary structures generated (e.g. parsed ASTs). Temporarily
-increasing `gc-cons-threshold' will help reduce the number of GC
-operations, at the cost of temporary memory usage.
+During `org-roam-db-sync', Emacs can pause multiple times to
+perform garbage collection because of the large number of
+temporary structures generated (e.g. parsed ASTs).
 
-This defaults to the original value of `gc-cons-threshold', but
-tweaking this number may lead to better overall performance. For
-example, to reduce the number of GCs, one may set it to a large
-value like `most-positive-fixnum'."
+`gc-cons-threshold' is temporarily set to
+`org-roam-db-gc-threshold' during this operation, and increasing
+`gc-cons-threshold' will help reduce the number of GC operations,
+at the cost of memory usage. Tweaking this value may lead to
+better overall performance.
+
+For example, to reduce the number of GCs to the minimum, on
+machines with large memory one may set it to
+`most-positive-fixnum'."
   :type 'int
   :group 'org-roam)
 
 (defcustom org-roam-db-node-include-function (lambda () t)
-  "A custom function to check if the headline at point is a node."
+  "A custom function to check if the point contains a valid node.
+This function is called each time a node (both file and headline)
+is about to be saved into the Org-roam database.
+
+If the function returns nil, Org-roam will skip the node. This
+function is useful for excluding certain nodes from the Org-roam
+database."
   :type 'function
   :group 'org-roam)
 
-(defconst org-roam-db-version 16)
-(defconst org-roam--sqlite-available-p
-  (with-demoted-errors "Org-roam initialization: %S"
-    (emacsql-sqlite-ensure-binary)
-    t))
+(defcustom org-roam-db-update-on-save t
+  "If t, update the Org-roam database upon saving the file.
+Disable this if your files are large and updating the database is
+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)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
 
-;;;; Core Functions
-
+;;; Core Functions
 (defun org-roam-db--get-connection ()
   "Return the database connection, if any."
-  (gethash (expand-file-name org-roam-directory)
+  (gethash (expand-file-name (file-name-as-directory org-roam-directory))
            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")
+
+(defun org-roam-db--conn-fn ()
+  "Return the function for creating the database connection."
+  (cl-case org-roam-database-connector
+    (sqlite
+     (progn
+       (require 'emacsql-sqlite)
+       #'emacsql-sqlite))
+    (libsqlite3
+     (progn
+       (require 'emacsql-libsqlite3)
+       #'emacsql-libsqlite3))
+    (sqlite3
+     (progn
+       (require 'emacsql-sqlite3)
+       #'emacsql-sqlite3))))
+
 (defun org-roam-db ()
   "Entrypoint to the Org-roam sqlite database.
 Initializes and stores the database, and the database connection.
@@ -107,9 +164,11 @@ Performs a database upgrade when required."
                (emacsql-live-p (org-roam-db--get-connection)))
     (let ((init-db (not (file-exists-p org-roam-db-location))))
       (make-directory (file-name-directory org-roam-db-location) t)
-      (let ((conn (emacsql-sqlite org-roam-db-location)))
-        (set-process-query-on-exit-flag (emacsql-process conn) nil)
-        (puthash (expand-file-name org-roam-directory)
+      (let ((conn (funcall (org-roam-db--conn-fn) org-roam-db-location)))
+        (emacsql conn [:pragma (= foreign_keys ON)])
+        (when-let ((process (emacsql-process conn)))
+          (set-process-query-on-exit-flag process nil))
+        (puthash (expand-file-name (file-name-as-directory org-roam-directory))
                  conn
                  org-roam-db--connection)
         (when init-db
@@ -128,7 +187,7 @@ Performs a database upgrade when required."
                    "and there is no upgrade path")))))))
   (org-roam-db--get-connection))
 
-;;;; Entrypoint: (org-roam-db-query)
+;;; Entrypoint: (org-roam-db-query)
 (define-error 'emacsql-constraint "SQL constraint violation")
 (defun org-roam-db-query (sql &rest args)
   "Run SQL query on Org-roam database with ARGS.
@@ -144,10 +203,11 @@ The query is expected to be able to fail, in this situation, run HANDLER."
     (emacsql-constraint
      (funcall handler err))))
 
-;;;; Schemata
+;;; Schemata
 (defconst org-roam-db--table-schemata
   '((files
      [(file :unique :primary-key)
+      title
       (hash :not-null)
       (atime :not-null)
       (mtime :not-null)])
@@ -171,6 +231,13 @@ The query is expected to be able to fail, in this situation, run HANDLER."
        alias]
       (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
 
+    (citations
+     ([(node-id :not-null)
+       (cite-key :not-null)
+       (pos :not-null)
+       properties]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
     (refs
      ([(node-id :not-null)
        (ref :not-null)
@@ -198,7 +265,6 @@ 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-with-transaction db
-    (emacsql db "PRAGMA foreign_keys = ON")
     (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
       (emacsql db [:create-table $i1 $S2] table schema))
     (pcase-dolist (`(,index-name ,table ,columns) org-roam-db--table-indices)
@@ -230,8 +296,8 @@ the current `org-roam-directory'."
   (dolist (conn (hash-table-values org-roam-db--connection))
     (org-roam-db--close conn)))
 
-;;;; Database API
-;;;;; Clearing
+;;; Database API
+;;;; Clearing
 (defun org-roam-db-clear-all ()
   "Clears all entries in the Org-roam cache."
   (interactive)
@@ -248,11 +314,23 @@ If FILE is nil, clear the current buffer."
                       :where (= file $s1)]
                      file))
 
-;;;;; Updating tables
+;;;; Updating tables
+
+(defun org-roam-db--file-title ()
+  "In current Org buffer, get the title.
+If there is no title, return the file name relative to
+`org-roam-directory'."
+  (org-link-display-format
+   (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))))
+       (file-name-sans-extension (file-relative-name
+                                  (buffer-file-name (buffer-base-buffer))
+                                  org-roam-directory)))))
+
 (defun org-roam-db-insert-file ()
   "Update the files table for the current buffer.
 If UPDATE-P is non-nil, first remove the file in the database."
   (let* ((file (buffer-file-name))
+         (file-title (org-roam-db--file-title))
          (attr (file-attributes file))
          (atime (file-attribute-access-time attr))
          (mtime (file-attribute-modification-time attr))
@@ -260,7 +338,7 @@ If UPDATE-P is non-nil, first remove the file in the database."
     (org-roam-db-query
      [:insert :into files
       :values $v1]
-     (list (vector file hash atime mtime)))))
+     (list (vector file file-title hash atime mtime)))))
 
 (defun org-roam-db-get-scheduled-time ()
   "Return the scheduled time at point in ISO8601 format."
@@ -273,27 +351,59 @@ If UPDATE-P is non-nil, first remove the file in the database."
     (org-format-time-string "%FT%T%z" time)))
 
 (defun org-roam-db-node-p ()
-  "Return t if headline at point is a node, else return nil."
+  "Return t if headline at point is an Org-roam node, else return nil."
   (and (org-id-get)
-       (not (cdr (assoc "ROAM_EXCLUDE" (org-entry-properties))))
+       (not (org-entry-get (point) "ROAM_EXCLUDE"))
        (funcall org-roam-db-node-include-function)))
 
 (defun org-roam-db-map-nodes (fns)
   "Run FNS over all nodes in the current buffer."
-  (org-with-point-at 1
-    (org-map-entries
-     (lambda ()
-       (when (org-roam-db-node-p)
-         (dolist (fn fns)
-           (funcall fn)))))))
+  (org-map-region
+   (lambda ()
+     (when (org-roam-db-node-p)
+       (dolist (fn fns)
+         (funcall fn))))
+   (point-min) (point-max)))
 
 (defun org-roam-db-map-links (fns)
   "Run FNS over all links in the current buffer."
   (org-with-point-at 1
-    (org-element-map (org-element-parse-buffer) 'link
-      (lambda (link)
-        (dolist (fn fns)
-          (funcall fn link))))))
+    (while (re-search-forward org-link-any-re nil :no-error)
+      ;; `re-search-forward' let the cursor one character after the link, we need to go backward one char to
+      ;; make the point be on the link.
+      (backward-char)
+      (let* ((element (org-element-context))
+             (type (org-element-type element))
+             link bounds)
+        (cond
+         ;; Links correctly recognized by Org Mode
+         ((eq type 'link)
+          (setq link element))
+         ;; 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 (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)
+                           (cdr bounds))))
+          (with-temp-buffer
+            (delay-mode-hooks (org-mode))
+            (insert link)
+            (setq link (org-element-context)))))
+        (when link
+          (dolist (fn fns)
+            (funcall fn link)))))))
+
+(defun org-roam-db-map-citations (info fns)
+  "Run FNS over all citations in the current buffer.
+INFO is the org-element parsed buffer."
+  (org-element-map info 'citation-reference
+    (lambda (cite)
+      (dolist (fn fns)
+        (funcall fn cite)))))
 
 (defun org-roam-db-insert-file-node ()
   "Insert the file-level node into the Org-roam cache."
@@ -302,21 +412,16 @@ If UPDATE-P is non-nil, first remove the file in the database."
                (org-roam-db-node-p))
       (when-let ((id (org-id-get)))
         (let* ((file (buffer-file-name (buffer-base-buffer)))
-               (title (org-link-display-format
-                       (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))
-                                        #'string-equal))
-                           (file-relative-name file org-roam-directory))))
+               (title (org-roam-db--file-title))
                (pos (point))
                (todo nil)
                (priority nil)
                (scheduled nil)
                (deadline nil)
                (level 0)
-               (aliases (org-entry-get (point) "ROAM_ALIASES"))
                (tags org-file-tags)
-               (refs (org-entry-get (point) "ROAM_REFS"))
                (properties (org-entry-properties))
-               (olp (org-get-outline-path)))
+               (olp nil))
           (org-roam-db-query!
            (lambda (err)
              (lwarn 'org-roam :warning "%s for %s (%s) in %s"
@@ -333,31 +438,10 @@ If UPDATE-P is non-nil, first remove the file in the database."
              (mapcar (lambda (tag)
                        (vector id (substring-no-properties tag)))
                      tags)))
-          (when aliases
-            (org-roam-db-query
-             [:insert :into aliases
-              :values $v1]
-             (mapcar (lambda (alias)
-                       (vector id alias))
-                     (split-string-and-unquote aliases))))
-          (when refs
-            (setq refs (split-string-and-unquote refs))
-            (let (rows)
-              (dolist (ref refs)
-                (if (string-match org-link-plain-re ref)
-                    (progn
-                      (push (vector id (match-string 2 ref)
-                                    (match-string 1 ref)) rows))
-                  (lwarn '(org-roam) :warning
-                         "%s:%s\tInvalid ref %s, skipping..."
-                         (buffer-file-name) (point) ref)))
-              (when rows
-                (org-roam-db-query
-                 [:insert :into refs
-                  :values $v1]
-                 rows)))))))))
+          (org-roam-db-insert-aliases)
+          (org-roam-db-insert-refs))))))
 
-(defun org-roam-db-insert-node-data ()
+(cl-defun org-roam-db-insert-node-data ()
   "Insert node data for headline at point into the Org-roam cache."
   (when-let ((id (org-id-get)))
     (let* ((file (buffer-file-name (buffer-base-buffer)))
@@ -368,9 +452,15 @@ If UPDATE-P is non-nil, first remove the file in the database."
            (level (nth 1 heading-components))
            (scheduled (org-roam-db-get-scheduled-time))
            (deadline (org-roam-db-get-deadline-time))
-           (title (org-link-display-format (nth 4 heading-components)))
+           (title (or (nth 4 heading-components)
+                      (progn (lwarn 'org-roam :warning "Node in %s:%s:%s has no title, skipping..."
+                                    file
+                                    (line-number-at-pos)
+                                    (1+ (- (point) (line-beginning-position))))
+                             (cl-return-from org-roam-db-insert-node-data))))
            (properties (org-entry-properties))
-           (olp (org-get-outline-path)))
+           (olp (org-get-outline-path nil 'use-cache))
+           (title (org-link-display-format title)))
       (org-roam-db-query!
        (lambda (err)
          (lwarn 'org-roam :warning "%s for %s (%s) in %s"
@@ -383,13 +473,14 @@ If UPDATE-P is non-nil, first remove the file in the database."
 
 (defun org-roam-db-insert-aliases ()
   "Insert aliases for node at point into Org-roam cache."
-  (when-let ((node-id (org-id-get))
-             (aliases (org-entry-get (point) "ROAM_ALIASES")))
+  (when-let* ((node-id (org-id-get))
+              (aliases (org-entry-get (point) "ROAM_ALIASES"))
+              (aliases (split-string-and-unquote aliases)))
     (org-roam-db-query [:insert :into aliases
                         :values $v1]
                        (mapcar (lambda (alias)
                                  (vector node-id alias))
-                               (split-string-and-unquote aliases)))))
+                               aliases))))
 
 (defun org-roam-db-insert-tags ()
   "Insert tags for node at point into Org-roam cache."
@@ -408,30 +499,81 @@ If UPDATE-P is non-nil, first remove the file in the database."
     (let (rows)
       (dolist (ref refs)
         (save-match-data
-          (if (string-match org-link-plain-re ref)
-              (progn
-                (push (vector node-id (match-string 2 ref) (match-string 1 ref)) rows))
-            (lwarn '(org-roam) :warning
-                   "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref))))
-      (org-roam-db-query [:insert :into refs
-                          :values $v1]
-                         rows))))
+          (cond (;; @citeKey
+                 (string-prefix-p "@" ref)
+                 (push (vector node-id (substring ref 1) "cite") rows))
+                (;; [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)
+                            (or (assoc link-type org-ref-cite-types)
+                                (member link-type org-ref-cite-types)))
+                       (dolist (key (org-roam-org-ref-path-to-keys path))
+                         (push (vector node-id key link-type) rows))
+                     (push (vector node-id path link-type) rows))))
+                (t
+                 (lwarn '(org-roam) :warning
+                        "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref)))))
+      (when rows
+        (org-roam-db-query [:insert :into refs
+                            :values $v1]
+                           rows)))))
 
 (defun org-roam-db-insert-link (link)
   "Insert link data for LINK at current point into the Org-roam cache."
   (save-excursion
     (goto-char (org-element-property :begin link))
     (let ((type (org-element-property :type link))
-          (dest (org-element-property :path link))
-          (properties (list :outline (org-get-outline-path)))
-          (source (org-roam-id-at-point)))
-      (when source
-        (org-roam-db-query
-         [:insert :into links
-          :values $v1]
-         (vector (point) source dest type properties))))))
+          (path (org-element-property :path link))
+          (source (org-roam-id-at-point))
+          (properties (list :outline (ignore-errors
+                                       ;; This can error if link is not under any headline
+                                       (org-get-outline-path 'with-self 'use-cache)))))
+      ;; For Org-ref links, we need to split the path into the cite keys
+      (when (and source path)
+        (if (and (boundp 'org-ref-cite-types)
+                 (or (assoc type org-ref-cite-types)
+                     (member type org-ref-cite-types)))
+            (org-roam-db-query
+             [:insert :into citations
+              :values $v1]
+             (mapcar (lambda (k) (vector source k (point) properties))
+                     (org-roam-org-ref-path-to-keys path)))
+          (org-roam-db-query
+           [:insert :into links
+            :values $v1]
+           (vector (point) source path type properties)))))))
 
-;;;;; Fetching
+(defun org-roam-db-insert-citation (citation)
+  "Insert data for CITATION at current point into the Org-roam cache."
+  (save-excursion
+    (goto-char (org-element-property :begin citation))
+    (let ((key (org-element-property :key citation))
+          (source (org-roam-id-at-point))
+          (properties (list :outline (ignore-errors
+                                       ;; This can error if link is not under any headline
+                                       (org-get-outline-path 'with-self 'use-cache)))))
+      (when (and source key)
+        (org-roam-db-query
+         [:insert :into citations
+          :values $v1]
+         (vector source key (point) properties))))))
+
+;;;; Fetching
 (defun org-roam-db--get-current-files ()
   "Return a hash-table of file to the hash of its file contents."
   (let ((current-files (org-roam-db-query [:select [file hash] :from files]))
@@ -442,6 +584,10 @@ If UPDATE-P is non-nil, first remove the file in the database."
 
 (defun org-roam-db--file-hash (&optional file-path)
   "Compute the hash of FILE-PATH, a file or current buffer."
+  ;; If it is a GPG encrypted file, we always want to compute the hash
+  ;; for the GPG encrypted file (undecrypted)
+  (when (and (not file-path) (equal "gpg" (file-name-extension (buffer-file-name))))
+    (setq file-path (buffer-file-name)))
   (if file-path
       (with-temp-buffer
         (set-buffer-multibyte nil)
@@ -450,18 +596,61 @@ If UPDATE-P is non-nil, first remove the file in the database."
     (org-with-wide-buffer
      (secure-hash 'sha1 (current-buffer)))))
 
-;;;;; Updating
+;;;; Synchronization
+(defun org-roam-db-update-file (&optional file-path no-require)
+  "Update Org-roam cache for FILE-PATH.
+
+If the file does not exist anymore, remove it from the cache.
+
+If the file exists, update the cache with information.
+
+If NO-REQUIRE, don't require optional libraries. Set NO-REQUIRE
+when the libraries are already required at some toplevel, e.g.
+in `org-roam-db-sync'."
+  (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
+  (let ((content-hash (org-roam-db--file-hash file-path))
+        (db-hash (caar (org-roam-db-query [:select hash :from files
+                                           :where (= file $s1)] file-path)))
+        info)
+    (unless (string= content-hash db-hash)
+      (unless no-require
+        (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)))))))))
+
 ;;;###autoload
 (defun org-roam-db-sync (&optional force)
   "Synchronize the cache state with the current Org files on-disk.
 If FORCE, force a rebuild of the cache from scratch."
   (interactive "P")
-  (when force (delete-file org-roam-db-location))
   (org-roam-db--close) ;; Force a reconnect
+  (when force (delete-file org-roam-db-location))
   (org-roam-db) ;; To initialize the database, no-op if already initialized
+  (org-roam-require '(org-ref oc))
   (let* ((gc-cons-threshold org-roam-db-gc-threshold)
          (org-agenda-files nil)
-         (org-roam-files (org-roam--list-all-files))
+         (org-roam-files (org-roam-list-files))
          (current-files (org-roam-db--get-current-files))
          (modified-files nil))
     (dolist (file org-roam-files)
@@ -471,49 +660,102 @@ If FORCE, force a rebuild of the cache from scratch."
           (push file modified-files)))
       (remhash file current-files))
     (emacsql-with-transaction (org-roam-db)
-      (if (fboundp 'dolist-with-progress-reporter)
-          (dolist-with-progress-reporter (file (hash-table-keys current-files))
-              "Clearing removed files..."
-            (org-roam-db-clear-file file))
-        (dolist (file (hash-table-keys current-files))
-          (org-roam-db-clear-file file)))
-      (if (fboundp 'dolist-with-progress-reporter)
-          (dolist-with-progress-reporter (file modified-files)
-              "Processing modified files..."
-            (org-roam-db-update-file file))
-        (dolist (file modified-files)
-          (org-roam-db-update-file file))))))
+      (org-roam-dolist-with-progress (file (hash-table-keys current-files))
+          "Clearing removed files..."
+        (org-roam-db-clear-file file))
+      (org-roam-dolist-with-progress (file modified-files)
+          "Processing modified files..."
+        (condition-case err
+            (org-roam-db-update-file file 'no-require)
+          (error
+           (org-roam-db-clear-file file)
+           (lwarn 'org-roam :error "Failed to process %s with error %s, skipping..."
+                  file (error-message-string err))))))))
 
-(defun org-roam-db-update-file (&optional file-path)
-  "Update Org-roam cache for FILE-PATH.
-If the file does not exist anymore, remove it from the cache.
-If the file exists, update the cache with information."
-  (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
-  (let ((content-hash (org-roam-db--file-hash file-path))
-        (db-hash (caar (org-roam-db-query [:select hash :from files
-                                           :where (= file $s1)] file-path))))
-    (unless (string= content-hash db-hash)
-      (org-roam-with-file file-path nil
-        (save-excursion
-          (org-set-regexps-and-options 'tags-only)
-          (org-roam-db-clear-file)
-          (org-roam-db-insert-file)
-          (org-roam-db-insert-file-node)
-          (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))
-          (org-roam-db-map-links
-           (list #'org-roam-db-insert-link)))))))
+;;;###autoload
+(define-minor-mode org-roam-db-autosync-mode
+  "Global minor mode to keep your Org-roam session automatically synchronized.
+Through the session this will continue to setup your
+buffers (that are Org-roam file visiting), keep track of the
+related changes, maintain cache consistency and incrementally
+update the currently active database.
 
-(defun org-roam-db--update-on-save-h ()
-  "."
-  (add-hook 'after-save-hook #'org-roam-db-update-file nil t))
+If you need to manually trigger resync of the currently active
+database, see `org-roam-db-sync' command."
+  :group 'org-roam
+  :global t
+  :init-value nil
+  (let ((enabled org-roam-db-autosync-mode))
+    (cond
+     (enabled
+      (add-hook 'find-file-hook  #'org-roam-db-autosync--setup-file-h)
+      (add-hook 'kill-emacs-hook #'org-roam-db--close-all)
+      (advice-add #'rename-file :after  #'org-roam-db-autosync--rename-file-a)
+      (advice-add #'delete-file :before #'org-roam-db-autosync--delete-file-a)
+      (org-roam-db-sync))
+     (t
+      (remove-hook 'find-file-hook  #'org-roam-db-autosync--setup-file-h)
+      (remove-hook 'kill-emacs-hook #'org-roam-db--close-all)
+      (advice-remove #'rename-file #'org-roam-db-autosync--rename-file-a)
+      (advice-remove #'delete-file #'org-roam-db-autosync--delete-file-a)
+      (org-roam-db--close-all)
+      ;; Disable local hooks for all org-roam buffers
+      (dolist (buf (org-roam-buffer-list))
+        (with-current-buffer buf
+          (remove-hook 'after-save-hook #'org-roam-db-autosync--try-update-on-save-h t)))))))
 
-(add-hook 'org-roam-find-file-hook #'org-roam-db--update-on-save-h)
+;;;###autoload
+(defun org-roam-db-autosync-enable ()
+  "Activate `org-roam-db-autosync-mode'."
+  (org-roam-db-autosync-mode +1))
 
-;; Diagnostic Interactives
+(defun org-roam-db-autosync-disable ()
+  "Deactivate `org-roam-db-autosync-mode'."
+  (org-roam-db-autosync-mode -1))
+
+(defun org-roam-db-autosync-toggle ()
+  "Toggle `org-roam-db-autosync-mode' enabled/disabled."
+  (org-roam-db-autosync-mode 'toggle))
+
+(defun org-roam-db-autosync--delete-file-a (file &optional _trash)
+  "Maintain cache consistency when file deletes.
+FILE is removed from the database."
+  (when (and (not (auto-save-file-name-p file))
+             (not (backup-file-name-p file))
+             (org-roam-file-p file))
+    (org-roam-db-clear-file (expand-file-name file))))
+
+(defun org-roam-db-autosync--rename-file-a (old-file new-file-or-dir &rest _args)
+  "Maintain cache consistency of file rename.
+OLD-FILE is cleared from the database, and NEW-FILE-OR-DIR is added."
+  (let ((new-file (if (directory-name-p new-file-or-dir)
+                      (expand-file-name (file-name-nondirectory old-file) new-file-or-dir)
+                    new-file-or-dir)))
+    (setq new-file (expand-file-name new-file))
+    (setq old-file (expand-file-name old-file))
+    (when (and (not (auto-save-file-name-p old-file))
+               (not (auto-save-file-name-p new-file))
+               (not (backup-file-name-p old-file))
+               (not (backup-file-name-p new-file))
+               (org-roam-file-p old-file))
+      (org-roam-db-clear-file old-file))
+    (when (org-roam-file-p new-file)
+      (org-roam-db-update-file new-file))))
+
+(defun org-roam-db-autosync--setup-file-h ()
+  "Setup the current buffer if it visits an Org-roam file."
+  (when (org-roam-file-p) (run-hooks 'org-roam-find-file-hook)))
+
+(add-hook 'org-roam-find-file-hook #'org-roam-db-autosync--setup-update-on-save-h)
+(defun org-roam-db-autosync--setup-update-on-save-h ()
+  "Setup the current buffer to update the DB after saving the current file."
+  (add-hook 'after-save-hook #'org-roam-db-autosync--try-update-on-save-h nil t))
+
+(defun org-roam-db-autosync--try-update-on-save-h ()
+  "If appropriate, update the database for the current file after saving buffer."
+  (when org-roam-db-update-on-save (org-roam-db-update-file)))
+
+;;; Diagnostics
 (defun org-roam-db-diagnose-node ()
   "Print information about node at point."
   (interactive)

org-roam-macs.el

@@ -1,90 +0,0 @@
-;;; org-roam-macs.el --- Macros/utility functions -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 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: 2.0.0
-;; 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 "2.90.1"))
-
-;; 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 library implements macros used throughout org-roam.
-;;
-;;; Code:
-(defmacro org-roam-plist-map! (fn plist)
-  "Map FN over PLIST, modifying it in-place."
-  (declare (indent 1))
-  (let ((plist-var (make-symbol "plist"))
-        (k (make-symbol "k"))
-        (v (make-symbol "v")))
-    `(let ((,plist-var (copy-sequence ,plist)))
-       (while ,plist-var
-         (setq ,k (pop ,plist-var))
-         (setq ,v (pop ,plist-var))
-         (setq ,plist (plist-put ,plist ,k (funcall ,fn ,k ,v)))))))
-
-(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.
-Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
-  (declare (indent 2) (debug t))
-  `(let* (new-buf
-          (auto-mode-alist nil)
-          (buf (or (and (not ,file)
-                        (current-buffer)) ;If FILE is nil, use current buffer
-                   (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
-                   (progn
-                     (setq new-buf t)
-                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
-          res)
-     (with-current-buffer buf
-       (unless (equal major-mode 'org-mode)
-         (delay-mode-hooks
-           (let ((org-inhibit-startup t)
-                 (org-agenda-files nil))
-             (org-mode))))
-       (setq res (progn ,@body))
-       (unless (and new-buf (not ,keep-buf-p))
-         (save-buffer)))
-     (if (and new-buf (not ,keep-buf-p))
-       (when (find-buffer-visiting ,file)
-         (kill-buffer (find-buffer-visiting ,file))))
-     res))
-
-(defmacro org-roam-with-temp-buffer (file &rest body)
-  "Execute BODY within a temp buffer.
-Like `with-temp-buffer', but propagates `org-roam-directory'.
-If FILE, set `default-directory' to FILE's directory and insert its contents."
-  (declare (indent 1) (debug t))
-  (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
-    `(let ((,current-org-roam-directory org-roam-directory))
-       (with-temp-buffer
-         (let ((org-roam-directory ,current-org-roam-directory))
-           (delay-mode-hooks (org-mode))
-           (when ,file
-             (insert-file-contents ,file)
-             (setq-local default-directory (file-name-directory ,file)))
-           ,@body)))))
-
-(provide 'org-roam-macs)
-
-;;; org-roam-macs.el ends here

org-roam-migrate.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; 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.
 
@@ -27,47 +27,14 @@
 
 ;;; Commentary:
 ;;
-;;  To ease transition from v1 to v2, we provide various migration utilities.
-;;  This library helps convert v1 notes to v2, and informs the user.
+;; This is a special library provided for the v1 users of this package. It's
+;; purpose is to ease the transition from v1 to v2, by providing migration
+;; utilities to convert from v1 notes to v2 nodes.
 ;;
 ;;; Code:
-;;;; Dependencies
-;;;;
-;;; v1 breaking warning
-(require 'org-roam-db)
-
-(defvar org-roam-v2-ack nil)
-
-(unless org-roam-v2-ack
-  (lwarn 'org-roam :error "
-------------------------------------
-WARNING: You're now on Org-roam v2!
-------------------------------------
-
-You may have arrived here from a package upgrade. Please read the
-wiki entry at
-https://github.com/org-roam/org-roam/wiki/Hitchhiker's-Rough-Guide-to-Org-roam-V2
-for an overview of the major changes.
-
-Notes taken in v1 are incompatible with v1, but you can upgrade
-them to the v2 format via a simple command. To migrate your
-notes, run:
-
-  M-x org-roam-migrate-wizard
-
-If you wish to stay on v1, v1 is unfortunately not distributed on
-MELPA. See org-roam/org-roam-v1 on GitHub on how to install v1.
-
-If you've gone through the migration steps (if necessary), and
-know what you're doing set `org-roam-v2-ack' to `t' to disable
-this warning. You can do so by adding:
-
-(setq org-roam-v2-ack t)
-
-To your init file.
-
-"))
+(require 'org-roam)
 
+;;; Migration wizard (v1 -> v2)
 ;;;###autoload
 (defun org-roam-migrate-wizard ()
   "Migrate all notes from to be compatible with Org-roam v2.
@@ -83,15 +50,19 @@ This will take a while. Are you sure you want to do this?")
       (message "Backing up files to %s" backup-dir)
       (copy-directory org-roam-directory backup-dir))
 
+    ;; Upgrade database to v2
+    (org-roam-db-sync 'force)
+
     ;; Convert v1 to v2
-    (dolist (f (org-roam--list-all-files))
+    (dolist (f (org-roam-list-files))
       (org-roam-with-file f nil
         (org-roam-migrate-v1-to-v2)))
+
     ;; Rebuild cache
     (org-roam-db-sync 'force)
 
     ;;Replace all file links with ID links
-    (dolist (f (org-roam--list-all-files))
+    (dolist (f (org-roam-list-files))
       (org-roam-with-file f nil
         (org-roam-migrate-replace-file-links-with-id)
         (save-buffer)))))
@@ -126,7 +97,11 @@ This will take a while. Are you sure you want to do this?")
   ;; Replace #+roam_tags into #+filetags
   (org-with-point-at 1
     (let* ((roam-tags (org-roam-migrate-get-prop-list "ROAM_TAGS"))
-           (file-tags (org-roam-migrate-get-prop-list "FILETAGS"))
+           (file-tags (cl-mapcan (lambda (value)
+                                   (cl-mapcan
+                                    (lambda (k) (org-split-string k ":"))
+                                    (split-string value)))
+                                 (org-roam-migrate-get-prop-list "FILETAGS")))
            (tags (append roam-tags file-tags))
            (tags (seq-map (lambda (tag)
                             (replace-regexp-in-string
@@ -135,7 +110,7 @@ This will take a while. Are you sure you want to do this?")
                              tag)) tags))
            (tags (seq-uniq tags)))
       (when tags
-        (org-roam-migrate-prop-set "filetags" (string-join tags " "))))
+        (org-roam-migrate-prop-set "filetags" (org-make-tag-string tags))))
     (let ((case-fold-search t))
       (org-with-point-at 1
         (while (re-search-forward "^#\\+roam_tags:" (point-max) t)
@@ -186,7 +161,8 @@ If the property is already set, replace its value."
                                                         :where (= file $s1)
                                                         :and (= level 0)] path))))
             (set-match-data mdata)
-            (replace-match (org-link-make-string (concat "id:" node-id)) nil t)))))))
+            (replace-match (org-link-make-string (concat "id:" node-id)
+                                                 desc) nil t)))))))
 
 (provide 'org-roam-migrate)
 ;;; org-roam-migrate.el ends here

org-roam-mode.el

@@ -1,11 +1,12 @@
-;;; org-roam-mode.el --- create and refresh Org-roam buffers -*- lexical-binding: t -*-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- 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: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; 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.
 
@@ -26,18 +27,50 @@
 
 ;;; Commentary:
 ;;
-;; This library implements the abstract major-mode `org-roam-mode', from which
-;; almost all other Org-roam major-modes derive.
+;; This module implements `org-roam-mode', which is a major mode that used by
+;; special Org-roam buffers to display various content in a section-like manner
+;; about the nodes and relevant to them information (e.g. backlinks) with which
+;; the user can interact with.
 ;;
 ;;; Code:
-(require 'magit-section)
+(require 'org-roam)
 
-(require 'org-roam-utils)
+;;;; Declarations
+(defvar org-ref-buffer-hacked)
 
-(defvar org-roam-directory)
-(defvar org-roam-find-file-hook)
+;;; 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'."
+  :group 'org-roam
+  :type 'hook)
 
-(declare-function org-roam-node-at-point "org-roam")
+(defcustom org-roam-buffer-postrender-functions (list)
+  "Functions to run after the Org-roam buffer is rendered.
+Each function accepts no arguments, and is run with the Org-roam
+buffer as the current buffer."
+  :group 'org-roam
+  :type 'hook)
+
+(defcustom org-roam-preview-function #'org-roam-preview-default-function
+  "The preview function to use to populate the Org-roam buffer.
+
+The function takes no arguments, but the point is temporarily set
+to the exact location of the backlink."
+  :group 'org-roam
+  :type 'function)
+
+(defcustom org-roam-preview-postprocess-functions (list #'org-roam-strip-comments)
+  "A list of functions to postprocess the preview content.
+
+Each function takes a single argument, the string for the preview
+content, and returns the post-processed string. The functions are
+applied in order of appearance in the list."
+  :group 'org-roam
+  :type 'hook)
 
 ;;; Faces
 (defface org-roam-header-line
@@ -119,91 +152,152 @@ and `:slant'."
   "Face for the dimmer part of the widgets."
   :group 'org-roam-faces)
 
-;;; Variables
-(defvar org-roam-current-node nil
-  "The current node at point.")
-
-(defvar org-roam-current-directory nil
-  "The `org-roam-directory' value for the current node.")
-
-(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
-                                                 #'org-roam-reflinks-section)
-  "Functions which insert sections of the `org-roam-buffer'.
-Each function is called with one argument, which is the current org-roam node at point."
-  :group 'org-roam
-  :type 'hook)
-
-;;; The mode
+;;; Major mode
 (defvar org-roam-mode-map
   (let ((map (make-sparse-keymap)))
     (set-keymap-parent map magit-section-mode-map)
-    (define-key map [C-return]  'org-roam-visit-thing)
-    (define-key map (kbd "C-m") 'org-roam-visit-thing)
-    (define-key map [remap revert-buffer] 'org-roam-buffer-render)
+    (define-key map [C-return]  'org-roam-buffer-visit-thing)
+    (define-key map (kbd "C-m") 'org-roam-buffer-visit-thing)
+    (define-key map [remap revert-buffer] 'org-roam-buffer-refresh)
     map)
   "Parent keymap for all keymaps of modes derived from `org-roam-mode'.")
 
 (define-derived-mode org-roam-mode magit-section-mode "Org-roam"
-  "Major mode for Org-roam's buffer."
+  "Major mode for displaying relevant information about Org-roam nodes.
+This mode is used by special Org-roam buffers, such as persistent
+`org-roam-buffer' and dedicated Org-roam buffers
+\(`org-roam-buffer-display-dedicated'), which render the
+information in a section-like manner (see
+`org-roam-mode-section-functions'), with which the user can
+interact with."
   :group 'org-roam
   (face-remap-add-relative 'header-line 'org-roam-header-line))
 
-;;; Key functions
-(defun org-roam-visit-thing ()
+;;; Buffers
+(defvar org-roam-buffer-current-node nil
+  "The node for which an `org-roam-mode' based buffer displays its contents.
+This set both, locally and globally. Normally the local value is
+only set in the `org-roam-mode' based buffers, while the global
+value shows the current node in the persistent `org-roam-buffer'.")
+
+(put 'org-roam-buffer-current-node 'permanent-local t)
+
+(defvar org-roam-buffer-current-directory nil
+  "The `org-roam-directory' value of `org-roam-buffer-current-node'.
+Set both, locally and globally in the same way as
+`org-roam-buffer-current-node'.")
+
+(put 'org-roam-buffer-current-directory 'permanent-local t)
+
+;;;; Library
+(defun org-roam-buffer-visit-thing ()
   "This is a placeholder command.
 Where applicable, section-specific keymaps bind another command
 which visits the thing at point."
   (interactive)
   (user-error "There is no thing at point that could be visited"))
 
-(defun org-roam-buffer-render ()
-  "Render the current node at point."
-  (interactive)
-  (when (derived-mode-p 'org-roam-mode)
-    (let ((inhibit-read-only t))
-      (erase-buffer)
-      (setq-local default-directory org-roam-current-directory)
-      (setq-local org-roam-directory org-roam-current-directory)
-      (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
-      (magit-insert-section (org-roam)
-        (magit-insert-heading)
-        (run-hook-with-args 'org-roam-mode-section-functions org-roam-current-node)))))
+(defun org-roam-buffer-file-at-point (&optional assert)
+  "Return the file at point in the current `org-roam-mode' based buffer.
+If ASSERT, throw an error."
+  (if-let ((file (magit-section-case
+                   (org-roam-node-section (org-roam-node-file (oref it node)))
+                   (org-roam-grep-section (oref it file))
+                   (org-roam-preview-section (oref it file))
+                   (t (cl-assert (derived-mode-p 'org-roam-mode))))))
+      file
+    (when assert
+      (user-error "No file at point"))))
 
-(defun org-roam-buffer ()
-  "Launch an Org-roam buffer for the current node at point."
+(defun org-roam-buffer-refresh ()
+  "Refresh the contents of the currently selected Org-roam buffer."
   (interactive)
-  (if-let ((node (org-roam-node-at-point))
-           (source-org-roam-directory org-roam-directory))
-      (progn
-        (let ((buffer (get-buffer-create
-                       (concat "org-roam: "
-                               (file-relative-name (buffer-file-name) org-roam-directory)))))
-          (with-current-buffer buffer
-            (org-roam-mode)
-            (setq-local org-roam-current-node node)
-            (setq-local org-roam-current-directory source-org-roam-directory)
-            (org-roam-buffer-render))
-          (switch-to-buffer-other-window buffer)))
-    (user-error "No node at point")))
+  (cl-assert (derived-mode-p 'org-roam-mode))
+  (save-excursion (org-roam-buffer-render-contents)))
 
-;;; Persistent buffer
+(defun org-roam-buffer-render-contents ()
+  "Recompute and render the contents of an Org-roam buffer.
+Assumes that the current buffer is an `org-roam-mode' based
+buffer."
+  (let ((inhibit-read-only t))
+    (erase-buffer)
+    (org-roam-mode)
+    (setq-local default-directory org-roam-buffer-current-directory)
+    (setq-local org-roam-directory org-roam-buffer-current-directory)
+    (org-roam-buffer-set-header-line-format
+     (org-roam-node-title org-roam-buffer-current-node))
+    (magit-insert-section (org-roam)
+      (magit-insert-heading)
+      (run-hook-with-args 'org-roam-mode-section-functions org-roam-buffer-current-node))
+    (run-hooks 'org-roam-buffer-postrender-functions)
+    (goto-char 0)))
+
+(defun org-roam-buffer-set-header-line-format (string)
+  "Set the header-line using STRING.
+If the `face' property of any part of STRING is already set, then
+that takes precedence. Also pad the left side of STRING so that
+it aligns with the text area."
+  (setq-local header-line-format
+              (concat (propertize " " 'display '(space :align-to 0))
+                      string)))
+
+;;;; Dedicated buffer
+;;;###autoload
+(defun org-roam-buffer-display-dedicated (node)
+  "Launch NODE dedicated Org-roam buffer.
+Unlike the persistent `org-roam-buffer', the contents of this
+buffer won't be automatically changed and will be held in place.
+
+In interactive calls prompt to select NODE, unless called with
+`universal-argument', in which case NODE will be set to
+`org-roam-node-at-point'."
+  (interactive
+   (list (if current-prefix-arg
+             (org-roam-node-at-point 'assert)
+           (org-roam-node-read nil nil nil 'require-match))))
+  (let ((buffer (get-buffer-create (org-roam-buffer--dedicated-name node))))
+    (with-current-buffer buffer
+      (setq-local org-roam-buffer-current-node node)
+      (setq-local org-roam-buffer-current-directory org-roam-directory)
+      (org-roam-buffer-render-contents))
+    (display-buffer buffer)))
+
+(defun org-roam-buffer--dedicated-name (node)
+  "Construct buffer name for NODE dedicated Org-roam buffer."
+  (let ((title (org-roam-node-title node))
+        (filename (file-relative-name (org-roam-node-file node) org-roam-directory)))
+    (format "*org-roam: %s<%s>*" title filename)))
+
+(defun org-roam-buffer-dedicated-p (&optional buffer)
+  "Return t if an Org-roam BUFFER is a node dedicated one.
+See `org-roam-buffer-display-dedicated' for more details.
+If BUFFER is nil, default it to `current-buffer'."
+  (or buffer (setq buffer (current-buffer)))
+  (string-match-p (concat "^" (regexp-quote "*org-roam: "))
+                  (buffer-name buffer)))
+
+;;;; Persistent buffer
 (defvar org-roam-buffer "*org-roam*"
-  "The persistent Org-roam buffer name.")
+  "The persistent Org-roam buffer name. Must be surround with \"*\".
+The content inside of this buffer will be automatically updated
+to the nearest node at point that comes from the current buffer.
+To toggle its display use `org-roam-buffer-toggle' command.")
 
-(defun org-roam-buffer--post-command-h ()
-  "Reconstructs the Org-roam buffer.
-This needs to be quick or infrequent, because this is run at
-`post-command-hook'.  If REDISPLAY, force an update of
-the Org-roam buffer."
-  (when (get-buffer-window org-roam-buffer)
-    (when-let ((node (org-roam-node-at-point)))
-      (unless (equal node org-roam-current-node)
-        (setq org-roam-current-node node)
-        (setq org-roam-current-directory org-roam-directory)
-        (org-roam-buffer-persistent-redisplay)))))
+(defun org-roam-buffer-toggle ()
+  "Toggle display of the persistent `org-roam-buffer'."
+  (interactive)
+  (pcase (org-roam-buffer--visibility)
+    ('visible
+     (progn
+       (delete-window (get-buffer-window org-roam-buffer))
+       (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
+    ((or 'exists 'none)
+     (progn
+       (display-buffer (get-buffer-create org-roam-buffer))
+       (org-roam-buffer-persistent-redisplay)))))
 
 (define-inline org-roam-buffer--visibility ()
-  "Return whether the current visibility state of the org-roam buffer.
+  "Return the current visibility state of the persistent `org-roam-buffer'.
 Valid states are 'visible, 'exists and 'none."
   (declare (side-effect-free t))
   (inline-quote
@@ -212,44 +306,145 @@ Valid states are 'visible, 'exists and 'none."
     ((get-buffer org-roam-buffer) 'exists)
     (t 'none))))
 
-(defun org-roam-buffer-toggle ()
-  "Toggle display of the Org-roam buffer."
-  (interactive)
-  (pcase (org-roam-buffer--visibility)
-    ('visible
-     (progn
-       (delete-window (get-buffer-window org-roam-buffer))
-       (remove-hook 'post-command-hook #'org-roam-buffer--post-command-h)))
-    ((or 'exists 'none)
-     (progn
-       (setq org-roam-current-node (org-roam-node-at-point)
-             org-roam-current-directory org-roam-directory)
-       (display-buffer (get-buffer-create org-roam-buffer))
-       (org-roam-buffer-persistent-redisplay)))))
-
 (defun org-roam-buffer-persistent-redisplay ()
-  "Recompute contents of the persistent Org-roam buffer.
-Has no effect when `org-roam-current-node' is nil."
-  (when org-roam-current-node
-    (with-current-buffer (get-buffer-create org-roam-buffer)
-      (let ((inhibit-read-only t))
-        (erase-buffer)
-        (org-roam-mode)
-        (setq-local default-directory org-roam-current-directory)
-        (setq-local org-roam-directory org-roam-current-directory)
-        (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
-        (magit-insert-section (org-roam)
-          (magit-insert-heading)
-          (dolist (fn org-roam-mode-section-functions)
-            (funcall fn org-roam-current-node)))))))
+  "Recompute contents of the persistent `org-roam-buffer'.
+Has no effect when there's no `org-roam-node-at-point'."
+  (when-let ((node (org-roam-node-at-point)))
+    (unless (equal node org-roam-buffer-current-node)
+      (setq org-roam-buffer-current-node node
+            org-roam-buffer-current-directory org-roam-directory)
+      (with-current-buffer (get-buffer-create org-roam-buffer)
+        (org-roam-buffer-render-contents)
+        (add-hook 'kill-buffer-hook #'org-roam-buffer--persistent-cleanup-h nil t)))))
 
-(defun org-roam-buffer--redisplay ()
-  "."
-  (add-hook 'post-command-hook #'org-roam-buffer--post-command-h nil t))
+(defun org-roam-buffer--persistent-cleanup-h ()
+  "Clean-up global state thats dedicated for the persistent `org-roam-buffer'."
+  (setq-default org-roam-buffer-current-node nil
+                org-roam-buffer-current-directory nil))
 
-(add-hook 'org-roam-find-file-hook #'org-roam-buffer--redisplay)
+(add-hook 'org-roam-find-file-hook #'org-roam-buffer--setup-redisplay-h)
+(defun org-roam-buffer--setup-redisplay-h ()
+  "Setup automatic redisplay of the persistent `org-roam-buffer'."
+  (add-hook 'post-command-hook #'org-roam-buffer--redisplay-h nil t))
+
+(defun org-roam-buffer--redisplay-h ()
+  "Reconstruct the persistent `org-roam-buffer'.
+This needs to be quick or infrequent, because this designed to
+run at `post-command-hook'."
+  (and (get-buffer-window org-roam-buffer)
+       (org-roam-buffer-persistent-redisplay)))
 
 ;;; Sections
+;;;; Node
+(defvar org-roam-node-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map org-roam-mode-map)
+    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-node-visit)
+    map)
+  "Keymap for `org-roam-node-section's.")
+
+(defclass org-roam-node-section (magit-section)
+  ((keymap :initform 'org-roam-node-map)
+   (node :initform nil))
+  "A `magit-section' used by `org-roam-mode' to outline NODE in its own heading.")
+
+(cl-defun org-roam-node-insert-section (&key source-node point properties)
+  "Insert section for a link from SOURCE-NODE to some other node.
+The other node is normally `org-roam-buffer-current-node'.
+
+SOURCE-NODE is an `org-roam-node' that links or references with
+the other node.
+
+POINT is a character position where the link is located in
+SOURCE-NODE's file.
+
+PROPERTIES (a plist) contains additional information about the
+link.
+
+Despite the name, this function actually inserts 2 sections at
+the same time:
+
+1. `org-roam-node-section' for a heading that describes
+   SOURCE-NODE. Acts as a parent section of the following one.
+
+2. `org-roam-preview-section' for a preview content that comes
+   from SOURCE-NODE's file for the link (that references the
+   other node) at POINT. Acts a child section of the previous
+   one."
+  (magit-insert-section section (org-roam-node-section)
+    (let ((outline (if-let ((outline (plist-get properties :outline)))
+                       (mapconcat #'org-link-display-format outline " > ")
+                     "Top")))
+      (insert (concat (propertize (org-roam-node-title source-node)
+                                  'font-lock-face 'org-roam-title)
+                      (format " (%s)"
+                              (propertize outline 'font-lock-face 'org-roam-olp)))))
+    (magit-insert-heading)
+    (oset section node source-node)
+    (magit-insert-section section (org-roam-preview-section)
+      (insert (org-roam-fontify-like-in-org-mode
+               (org-roam-preview-get-contents (org-roam-node-file source-node) point))
+              "\n")
+      (oset section file (org-roam-node-file source-node))
+      (oset section point point)
+      (insert ?\n))))
+
+;;;; Preview
+(defvar org-roam-preview-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map org-roam-mode-map)
+    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-preview-visit)
+    map)
+  "Keymap for `org-roam-preview-section's.")
+
+(defclass org-roam-preview-section (magit-section)
+  ((keymap :initform 'org-roam-preview-map)
+   (file :initform nil)
+   (point :initform nil))
+  "A `magit-section' used by `org-roam-mode' to contain preview content.
+The preview content comes from FILE, and the link as at POINT.")
+
+(defun org-roam-preview-visit (file point &optional other-window)
+  "Visit FILE at POINT and return the visited buffer.
+With OTHER-WINDOW non-nil do so in another window.
+In interactive calls OTHER-WINDOW is set with
+`universal-argument'."
+  (interactive (list (org-roam-buffer-file-at-point 'assert)
+                     (oref (magit-current-section) point)
+                     current-prefix-arg))
+  (let ((buf (find-file-noselect file))
+        (display-buffer-fn (if other-window
+                               #'switch-to-buffer-other-window
+                             #'pop-to-buffer-same-window)))
+    (funcall display-buffer-fn buf)
+    (with-current-buffer buf
+      (widen)
+      (goto-char point))
+    (when (org-invisible-p) (org-show-context))
+    buf))
+
+(defun org-roam-preview-default-function ()
+  "Return the preview content at point.
+
+This function returns the all contents under the current
+headline, up to the next headline."
+  (let ((beg (progn (org-roam-end-of-meta-data t)
+                    (point)))
+        (end (progn (org-next-visible-heading 1)
+                    (point))))
+    (string-trim (buffer-substring-no-properties beg end))))
+
+(defun org-roam-preview-get-contents (file pt)
+  "Get preview content for FILE at PT."
+  (save-excursion
+    (org-roam-with-temp-buffer file
+      (org-with-wide-buffer
+       (goto-char pt)
+       (let ((s (funcall org-roam-preview-function)))
+         (dolist (fn org-roam-preview-postprocess-functions)
+           (setq s (funcall fn s)))
+         s)))))
+
 ;;;; Backlinks
 (cl-defstruct (org-roam-backlink (:constructor org-roam-backlink-create)
                                  (:copier nil))
@@ -313,22 +508,27 @@ Sorts by title."
 
 (defun org-roam-reflinks-get (node)
   "Return the reflinks for NODE."
-  (let ((refs (org-roam-db-query [:select [ref] :from refs
-                                  :where (= node-id $s1)]
+  (let ((refs (org-roam-db-query [:select :distinct [refs:ref links:source links:pos links:properties]
+                                  :from refs
+                                  :left-join links
+                                  :where (= refs:node-id $s1)
+                                  :and (= links:dest refs:ref)
+                                  :union
+                                  :select :distinct [refs:ref citations:node-id
+                                                     citations:pos citations:properties]
+                                  :from refs
+                                  :left-join citations
+                                  :where (= refs:node-id $s1)
+                                  :and (= citations:cite-key refs:ref)]
                                  (org-roam-node-id node)))
         links)
-    (pcase-dolist (`(,ref) refs)
-      (pcase-dolist (`(,source-id ,pos ,properties) (org-roam-db-query
-                                                     [:select [source pos properties]
-                                                      :from links
-                                                      :where (= dest $s1)]
-                                                     ref))
-        (push (org-roam-populate
-               (org-roam-reflink-create
-                :source-node (org-roam-node-create :id source-id)
-                :ref ref
-                :point pos
-                :properties properties)) links)))
+    (pcase-dolist (`(,ref ,source-id ,pos ,properties) refs)
+      (push (org-roam-populate
+             (org-roam-reflink-create
+              :source-node (org-roam-node-create :id source-id)
+              :ref ref
+              :point pos
+              :properties properties)) links))
     links))
 
 (defun org-roam-reflinks-sort (a b)
@@ -339,22 +539,22 @@ Sorts by title."
 
 (defun org-roam-reflinks-section (node)
   "The reflinks section for NODE."
-  (when (org-roam-node-refs node)
-    (let* ((reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
-      (magit-insert-section (org-roam-reflinks)
-        (magit-insert-heading "Reflinks:")
-        (dolist (reflink reflinks)
-          (org-roam-node-insert-section
-           :source-node (org-roam-reflink-source-node reflink)
-           :point (org-roam-reflink-point reflink)
-           :properties (org-roam-reflink-properties reflink)))
-        (insert ?\n)))))
+  (when-let ((refs (org-roam-node-refs node))
+             (reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
+    (magit-insert-section (org-roam-reflinks)
+      (magit-insert-heading "Reflinks:")
+      (dolist (reflink reflinks)
+        (org-roam-node-insert-section
+         :source-node (org-roam-reflink-source-node reflink)
+         :point (org-roam-reflink-point reflink)
+         :properties (org-roam-reflink-properties reflink)))
+      (insert ?\n))))
 
-;;;; Unlinked references
+;;;; Grep
 (defvar org-roam-grep-map
   (let ((map (make-sparse-keymap)))
     (set-keymap-parent map org-roam-mode-map)
-    (define-key map [remap org-roam-visit-thing] 'org-roam-file-visit)
+    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-grep-visit)
     map)
   "Keymap for Org-roam grep result sections.")
 
@@ -362,29 +562,23 @@ Sorts by title."
   ((keymap :initform 'org-roam-grep-map)
    (file :initform nil)
    (row :initform nil)
-   (col :initform nil)))
+   (col :initform nil))
+  "A `magit-section' used by `org-roam-mode' to contain grep output.")
 
-(defun org-roam-file-at-point (&optional assert)
-  "Return the file at point.
-If ASSERT, throw an error."
-  (if-let ((file (magit-section-case
-                   (org-roam-node-section (org-roam-node-file (oref it node)))
-                   (org-roam-grep-section (oref it file))
-                   (org-roam-preview-section (oref it file)))))
-      file
-    (when assert
-      (user-error "No file at point"))))
-
-(defun org-roam-file-visit (file &optional other-window row col)
-  "Visits FILE.
-With a prefix argument OTHER-WINDOW, display the buffer in
-another window instead.
-If ROW, move to the row, and if COL move to the COL."
-  (interactive (list (org-roam-file-at-point t)
+(defun org-roam-grep-visit (file &optional other-window row col)
+  "Visit FILE at row ROW (if any) and column COL (if any). Return the buffer.
+With OTHER-WINDOW non-nil (in interactive calls set with
+`universal-argument') display the buffer in another window
+instead."
+  (interactive (list (org-roam-buffer-file-at-point t)
                      current-prefix-arg
                      (oref (magit-current-section) row)
                      (oref (magit-current-section) col)))
-  (let ((buf (find-file-noselect file)))
+  (let ((buf (find-file-noselect file))
+        (display-buffer-fn (if other-window
+                               #'switch-to-buffer-other-window
+                             #'pop-to-buffer-same-window)))
+    (funcall display-buffer-fn buf)
     (with-current-buffer buf
       (widen)
       (goto-char (point-min))
@@ -392,10 +586,10 @@ If ROW, move to the row, and if COL move to the COL."
         (forward-line (1- row)))
       (when col
         (forward-char (1- col))))
-    (funcall (if other-window
-                 #'switch-to-buffer-other-window
-               #'pop-to-buffer-same-window) buf)))
+    (when (org-invisible-p) (org-show-context))
+    buf))
 
+;;;; Unlinked references
 (defvar org-roam-unlinked-references-result-re
   (rx (group (one-or-more anything))
       ":"
@@ -410,7 +604,7 @@ If ROW, move to the row, and if COL move to the COL."
   "Return the preview line from FILE.
 This is the ROW within FILE."
   (with-temp-buffer
-    (insert-file-contents-literally file)
+    (insert-file-contents file)
     (forward-line (1- row))
     (buffer-substring-no-properties
      (save-excursion
@@ -449,14 +643,14 @@ 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)
                   (oset section row row)
                   (oset section col col)
                   (insert (propertize (format "%s:%s:%s"
-                                              (truncate-string-to-width (file-name-base f) 15 nil nil "...")
+                                              (truncate-string-to-width (file-name-base f) 15 nil nil t)
                                               row col) 'font-lock-face 'org-roam-dim)
                           " "
                           (org-roam-fontify-like-in-org-mode

org-roam-protocol.el

@@ -1,107 +0,0 @@
-;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 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: 2.0.0
-;; 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 "2.90.1"))
-
-;; 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:
-;;
-;; We extend org-protocol, adding custom Org-roam handlers. The setup
-;; instructions for `org-protocol' can be found in org-protocol.el.
-;;
-;; We define 2 protocols:
-;;
-;; 1. "roam-node": This protocol simply opens the node given by the node ID
-;; 2. "roam-ref": This protocol creates or opens a note with the given REF
-;;
-;;; Code:
-(require 'org-protocol)
-(require 'org-roam)
-(eval-when-compile
-  (require 'org-roam-macs))
-(require 'ol) ;; for org-link-decode
-
-(defcustom org-roam-protocol-store-links nil
-  "Whether to store links when capturing websites with `org-roam-protocol'."
-  :type 'boolean
-  :group 'org-roam)
-
-;;;; Functions
-(defun org-roam-protocol-open-ref (info)
-  "Process an org-protocol://roam-ref?ref= style url with INFO.
-
-It opens or creates a note with the given ref.
-
-  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
-        encodeURIComponent(location.href) + \\='&title=\\=' + \\
-        encodeURIComponent(document.title) + \\='&body=\\=' + \\
-        encodeURIComponent(window.getSelection())"
-  (unless (plist-get info :ref)
-    (user-error "No ref key provided"))
-  (org-roam-plist-map! (lambda (k v)
-                         (org-link-decode
-                          (if (equal k :ref)
-                              (org-protocol-sanitize-uri v)
-                            v))) info)
-  (when org-roam-protocol-store-links
-    (push (list (plist-get info :ref)
-                (plist-get info :title)) org-stored-links))
-  (org-link-store-props :type (and (string-match org-link-plain-re
-                                                 (plist-get info :ref))
-                                   (match-string 1 (plist-get info :ref)))
-                        :link (plist-get info :ref)
-                        :annotation (org-link-make-string (plist-get info :ref)
-                                                          (or (plist-get info :title)
-                                                              (plist-get info :ref)))
-                        :initial (or (plist-get info :body) ""))
-  (raise-frame)
-  (org-roam-capture-
-   :keys (plist-get info :template)
-   :node (org-roam-node-create :title (plist-get info :title))
-   :info (list :ref (plist-get info :ref)
-               :body (plist-get info :body))
-   :templates org-roam-capture-ref-templates)
-  nil)
-
-(defun org-roam-protocol-open-node (info)
-  "This handler simply opens the file with emacsclient.
-
-INFO is an alist containing additional information passed by the protocol URL.
-It should contain the FILE key, pointing to the path of the file to open.
-
-  Example protocol string:
-
-org-protocol://roam-node?node=uuid"
-  (when-let ((node (plist-get info :node)))
-    (raise-frame)
-    (org-roam-node-visit (org-roam-populate (org-roam-node-create :id node))))
-  nil)
-
-(push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
-      org-protocol-protocol-alist)
-(push '("org-roam-node"  :protocol "roam-node"   :function org-roam-protocol-open-node)
-      org-protocol-protocol-alist)
-
-(provide 'org-roam-protocol)
-
-;;; org-roam-protocol.el ends here

org-roam-utils.el

@@ -1,12 +1,12 @@
-;;; org-roam-utils.el --- Utilities for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-
 
-;; Copyright © 2020 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: 2.0.0
-;; 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 "2.90.1"))
+;; Version: 2.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,41 +27,21 @@
 
 ;;; Commentary:
 ;;
-;; This library implements utility functions used throughout
-;; Org-roam.
-;;
+;; This library provides definitions for utilities that used throughout the
+;; whole package.
 ;;
 ;;; Code:
-;;;; Library Requires
-(require 'dash)
 
-(eval-when-compile
-  (require 'org-roam-macs)
-  (require 'org-macs))
+(require 'org-roam)
 
-(defvar org-roam-verbose)
+(defun org-roam-require (libs)
+  "Require LIBS."
+  (dolist (lib libs)
+    (require lib nil 'noerror)))
 
-;; This is necessary to ensure all dependents on this module see
-;; `org-mode-hook' and `org-inhibit-startup' as dynamic variables,
-;; regardless of whether Org is loaded before their compilation.
-(require 'org)
-
-;;;; String Utilities
-(defun org-roam-truncate (len s &optional ellipsis)
-  "If S is longer than LEN, cut it down and add ELLIPSIS to the end.
-
-The resulting string, including ellipsis, will be LEN characters
-long.
-
-When not specified, ELLIPSIS defaults to ‘...’."
-  (declare (pure t) (side-effect-free t))
-  (unless ellipsis
-    (setq ellipsis "..."))
-  (if (> (length s) len)
-      (format "%s%s" (substring s 0 (- len (length ellipsis))) ellipsis)
-    s))
-
-(defun org-roam-replace (old new s)
+;;; String utilities
+;; TODO Refactor this.
+(defun org-roam-replace-string (old new s)
   "Replace OLD with NEW in S."
   (declare (pure t) (side-effect-free t))
   (replace-regexp-in-string (regexp-quote old) new s t t))
@@ -69,34 +49,152 @@ When not specified, ELLIPSIS defaults to ‘...’."
 (defun org-roam-quote-string (s)
   "Quotes string S."
   (->> s
-    (org-roam-replace "\\" "\\\\")
-    (org-roam-replace "\"" "\\\"")))
+       (org-roam-replace-string "\\" "\\\\")
+       (org-roam-replace-string "\"" "\\\"")))
 
-;;;; Utility Functions
-(defun org-roam--list-interleave (lst separator)
-  "Interleaves elements in LST with SEPARATOR."
-  (when lst
-    (let ((new-lst (list (pop lst))))
-      (dolist (it lst)
-        (nconc new-lst (list separator it)))
-      new-lst)))
+(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-up-heading-or-point-min ()
-  "Fixed version of Org's `org-up-heading-or-point-min'."
-  (ignore-errors (org-back-to-heading t))
-  (let ((p (point)))
-    (if (< 1 (funcall outline-level))
-        (progn
-          (org-up-heading-safe)
-          (when (= (point) p)
-            (goto-char (point-min))))
-      (unless (bobp) (goto-char (point-min))))))
+(defun org-roam-string-equal (s1 s2)
+  "Return t if S1 and S2 are equal.
+Like `string-equal', but case-insensitive."
+  (and (= (length s1) (length s2))
+       (or (string-equal s1 s2)
+           (string-equal (downcase s1) (downcase s2)))))
 
-(defun org-roam-message (format-string &rest args)
-  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
-  (when org-roam-verbose
-    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
+(defun org-roam-strip-comments (s)
+  "Strip Org comments from string S."
+  (with-temp-buffer
+    (insert s)
+    (goto-char (point-min))
+    (while (not (eobp))
+      (if (org-at-comment-p)
+          (delete-region (point-at-bol) (progn (forward-line) (point)))
+        (forward-line)))
+    (buffer-string)))
 
+;;; List utilities
+(defun org-roam-plist-map! (fn plist)
+  "Map FN over PLIST, modifying it in-place and returning it.
+FN must take two arguments: the key and the value."
+  (let ((plist-index plist))
+    (while plist-index
+      (let ((key (pop plist-index)))
+        (setf (car plist-index) (funcall fn key (car plist-index))
+              plist-index (cdr plist-index)))))
+  plist)
+
+(defmacro org-roam-dolist-with-progress (spec msg &rest body)
+  "Loop over a list and report progress in the echo area.
+Like `dolist-with-progress-reporter', but falls back to `dolist'
+if the function does not yet exist.
+
+Evaluate BODY with VAR bound to each car from LIST, in turn.
+Then evaluate RESULT to get return value, default nil.
+
+MSG is a progress reporter object or a string.  In the latter
+case, use this string to create a progress reporter.
+
+SPEC is a list, as per `dolist'."
+  (declare (indent 2))
+  (if (fboundp 'dolist-with-progress-reporter)
+      `(dolist-with-progress-reporter ,spec ,msg ,@body)
+    `(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 (expand-file-name b)
+                     (expand-file-name a))))
+
+(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.
+Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
+  (declare (indent 2) (debug t))
+  `(let* (new-buf
+          (auto-mode-alist nil)
+          (find-file-hook nil)
+          (buf (or (and (not ,file)
+                        (current-buffer)) ;If FILE is nil, use current buffer
+                   (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
+                   (progn
+                     (setq new-buf t)
+                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
+          res)
+     (with-current-buffer buf
+       (unless (derived-mode-p 'org-mode)
+         (delay-mode-hooks
+           (let ((org-inhibit-startup t)
+                 (org-agenda-files nil))
+             (org-mode)
+             (hack-local-variables))))
+       (setq res (progn ,@body))
+       (unless (and new-buf (not ,keep-buf-p))
+         (save-buffer)))
+     (if (and new-buf (not ,keep-buf-p))
+         (when (find-buffer-visiting ,file)
+           (kill-buffer (find-buffer-visiting ,file))))
+     res))
+
+;;; Buffer utilities
+(defmacro org-roam-with-temp-buffer (file &rest body)
+  "Execute BODY within a temp buffer.
+Like `with-temp-buffer', but propagates `org-roam-directory'.
+If FILE, set `default-directory' to FILE's directory and insert its contents."
+  (declare (indent 1) (debug t))
+  (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
+    `(let ((,current-org-roam-directory org-roam-directory))
+       (with-temp-buffer
+         (let ((org-roam-directory ,current-org-roam-directory))
+           (delay-mode-hooks (org-mode))
+           (when ,file
+             (insert-file-contents ,file)
+             (setq-local default-directory (file-name-directory ,file)))
+           ,@body)))))
+
+;;; Formatting
+(defun org-roam-format-template (template replacer)
+  "Format TEMPLATE with the function REPLACER.
+The templates are of form ${foo} for variable foo, and
+${foo=default} for variable foo with default value \"default\".
+REPLACER takes an argument of the format variable and the default
+value (possibly nil). Adapted from `s-format'."
+  (let ((saved-match-data (match-data)))
+    (unwind-protect
+        (replace-regexp-in-string
+         "\\${\\([^}]+\\)}"
+         (lambda (md)
+           (let ((var (match-string 1 md))
+                 (replacer-match-data (match-data))
+                 default-val)
+             (when (string-match "\\(.+\\)=\\(.+\\)" var)
+               (setq default-val (match-string 2 var)
+                     var (match-string 1 var)))
+             (unwind-protect
+                 (let ((v (progn
+                            (set-match-data saved-match-data)
+                            (funcall replacer var default-val))))
+                   (if v
+                       (format (apply #'propertize "%s" (text-properties-at 0 var)) v)
+                     (signal 'org-roam-format-resolve md)))
+               (set-match-data replacer-match-data))))
+         (if (functionp template)
+             (funcall template)
+           template)
+         ;; Need literal to make sure it works
+         t t)
+      (set-match-data saved-match-data))))
+
+;;; Fontification
 (defvar org-ref-buffer-hacked)
 
 (defun org-roam-fontify-like-in-org-mode (s)
@@ -125,38 +223,7 @@ Like `org-fontify-like-in-org-mode', but supports `org-ref'."
       (org-font-lock-ensure)
       (buffer-string))))
 
-(defun org-roam-set-header-line-format (string)
-  "Set the header-line using STRING.
-If the `face' property of any part of STRING is already set, then
-that takes precedence. Also pad the left side of STRING so that
-it aligns with the text area."
-  (setq-local header-line-format
-              (concat (propertize " " 'display '(space :align-to 0))
-                      string)))
-
-;;; Keywords
-(defun org-roam--get-keyword (name &optional bound)
-  "Return keyword property NAME in current buffer.
-If BOUND, scan up to BOUND bytes of the buffer."
-  (save-excursion
-    (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase name))))
-      (goto-char (point-min))
-      (when (re-search-forward re bound t)
-        (buffer-substring-no-properties (match-beginning 1) (match-end 1))))))
-
-(defun org-roam-get-keyword (name &optional file bound)
-  "Return keyword property NAME from an org FILE.
-FILE defaults to current file.
-Only scans up to BOUND bytes of the document."
-  (unless bound
-    (setq bound 1024))
-  (if file
-      (with-temp-buffer
-        (insert-file-contents-literally file nil 0 bound)
-        (org-roam--get-keyword name))
-    (org-roam--get-keyword name bound)))
-
-;;; Shielding regions
+;;;; Shielding regions
 (defface org-roam-shielded
   '((t :inherit (warning)))
   "Face for regions that are shielded (marked as read-only).
@@ -183,59 +250,100 @@ BEG and END are markers for the beginning and end regions."
                                              read-only t)
                             (marker-buffer beg))))
 
-;;; Formatting
-(defun org-roam-format (template replacer)
-  "Format TEMPLATE with the function REPLACER.
-REPLACER takes an argument of the format variable and optionally
-an extra argument which is the EXTRA value from the call to
-`org-roam-format'.
-Adapted from `s-format'."
-  (let ((saved-match-data (match-data)))
-    (unwind-protect
-        (replace-regexp-in-string
-         "\\${\\([^}]+\\)}"
-         (lambda (md)
-           (let ((var (match-string 1 md))
-                 (replacer-match-data (match-data)))
-             (unwind-protect
-                 (let ((v (progn
-                            (set-match-data saved-match-data)
-                            (funcall replacer var))))
-                   (if v (format "%s" v) (signal 'org-roam-format-resolve md)))
-               (set-match-data replacer-match-data)))) template
-         ;; Need literal to make sure it works
-         t t)
-      (set-match-data saved-match-data))))
+;;; Org-mode utilities
+;;;; Motions
+(defun org-roam-up-heading-or-point-min ()
+  "Fixed version of Org's `org-up-heading-or-point-min'."
+  (ignore-errors (org-back-to-heading t))
+  (let ((p (point)))
+    (if (< 1 (funcall outline-level))
+        (progn
+          (org-up-heading-safe)
+          (when (= (point) p)
+            (goto-char (point-min))))
+      (unless (bobp) (goto-char (point-min))))))
 
-(defvar org-roam--cached-display-format nil)
+;;;; Keywords
+(defun org-roam-get-keyword (name &optional file bound)
+  "Return keyword property NAME from an org FILE.
+FILE defaults to current file.
+Only scans up to BOUND bytes of the document."
+  (unless bound
+    (setq bound 1024))
+  (if file
+      (with-temp-buffer
+        (insert-file-contents file nil 0 bound)
+        (org-roam--get-keyword name))
+    (org-roam--get-keyword name bound)))
 
-(defun org-roam--process-display-format (format)
-  "Pre-calculate minimal widths needed by the FORMAT string."
-  (or org-roam--cached-display-format
-      (setq org-roam--cached-display-format
-            (let* ((fields-width 0)
-                   (string-width
-                    (string-width
-                     (org-roam-format
-                      format
-                      (lambda (field)
-                        (setq fields-width
-                              (+ fields-width
-                                 (string-to-number
-                                  (or (cadr (split-string field ":"))
-                                      "")))))))))
-              (cons format (+ fields-width string-width))))))
+(defun org-roam--get-keyword (name &optional bound)
+  "Return keyword property NAME in current buffer.
+If BOUND, scan up to BOUND bytes of the buffer."
+  (save-excursion
+    (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase name))))
+      (goto-char (point-min))
+      (when (re-search-forward re bound t)
+        (buffer-substring-no-properties (match-beginning 1) (match-end 1))))))
 
-;;; for org-roam-demote-entire-buffer in org-roam-refile.el
-(defun org-roam--file-keyword-get (keyword)
-  "Pull a KEYWORD setting from the top of the file.
+(defun org-roam-end-of-meta-data (&optional full)
+  "Like `org-end-of-meta-data', but supports file-level metadata.
 
-Keyword must be specified in ALL CAPS."
-  (cadr (assoc keyword
-               (org-collect-keywords (list keyword)))))
+When FULL is non-nil but not t, skip planning information,
+properties, clocking lines and logbook drawers.
 
-(defun org-roam--file-keyword-kill (keyword)
-  "Erase KEYWORD setting line from the top of the file."
+When optional argument FULL is t, skip everything above, and also
+skip keywords."
+  (org-back-to-heading-or-point-min t)
+  (when (org-at-heading-p) (forward-line))
+  ;; Skip planning information.
+  (when (looking-at-p org-planning-line-re) (forward-line))
+  ;; Skip property drawer.
+  (when (looking-at org-property-drawer-re)
+    (goto-char (match-end 0))
+    (forward-line))
+  ;; When FULL is not nil, skip more.
+  (when (and full (not (org-at-heading-p)))
+    (catch 'exit
+      (let ((end (save-excursion (outline-next-heading) (point)))
+            (re (concat "[ \t]*$" "\\|" org-clock-line-re)))
+        (while (not (eobp))
+          (cond ;; Skip clock lines.
+           ((looking-at-p re) (forward-line))
+           ;; Skip logbook drawer.
+           ((looking-at-p org-logbook-drawer-re)
+            (if (re-search-forward "^[ \t]*:END:[ \t]*$" end t)
+                (forward-line)
+              (throw 'exit t)))
+           ((looking-at-p org-drawer-regexp)
+            (if (re-search-forward "^[ \t]*:END:[ \t]*$" end t)
+                (forward-line)
+              (throw 'exit t)))
+           ;; When FULL is t, skip keywords too.
+           ((and (eq full t)
+                 (looking-at-p org-keyword-regexp))
+            (forward-line))
+           (t (throw 'exit t))))))))
+
+(defun org-roam-set-keyword (key value)
+  "Set keyword KEY to VALUE.
+If the property is already set, it's value is replaced."
+  (org-with-point-at 1
+    (let ((case-fold-search t))
+      (if (re-search-forward (concat "^#\\+" key ":\\(.*\\)") (point-max) t)
+          (if (string-blank-p value)
+              (kill-whole-line)
+            (replace-match (concat " " value) 'fixedcase nil nil 1))
+        (org-roam-end-of-meta-data 'drawers)
+        (if (save-excursion (end-of-line) (eobp))
+            (progn
+              (end-of-line)
+              (insert "\n"))
+          (forward-line)
+          (beginning-of-line))
+        (insert "#+" key ": " value "\n")))))
+
+(defun org-roam-erase-keyword (keyword)
+  "Erase the line where the KEYWORD is, setting line from the top of the file."
   (let ((case-fold-search t))
     (org-with-point-at 1
       (when (re-search-forward (concat "^#\\+" keyword ":") nil t)
@@ -243,39 +351,118 @@ Keyword must be specified in ALL CAPS."
         (delete-region (point) (line-end-position))
         (delete-char 1)))))
 
-(defun org-roam--kill-empty-buffer ()
-  "If the source buffer has been emptied, kill it.
+;;;; Properties
+(defun org-roam-add-property (val prop)
+  "Add VAL value to PROP property for the node at point.
+Both, VAL and PROP are strings."
+  (let* ((p (org-entry-get (point) prop))
+         (lst (when p (split-string-and-unquote p)))
+         (lst (if (memq val lst) lst (cons val lst)))
+         (lst (seq-uniq lst)))
+    (org-set-property prop (combine-and-quote-strings lst))
+    val))
 
-If the buffer is associated with a file, delete the file.
+(defun org-roam-remove-property (prop &optional val)
+  "Remove VAL value from PROP property for the node at point.
+Both VAL and PROP are strings.
 
-If the buffer is associated with an in-process capture operation, abort the operation."
-  (when (eq (buffer-size) 0)
-    (if (buffer-file-name)
-        (delete-file (buffer-file-name)))
-    (set-buffer-modified-p nil)
-    (when (and org-capture-mode
-               (buffer-base-buffer (current-buffer)))
-      (org-capture-kill))
-    (kill-buffer (current-buffer))))
+If VAL is not specified, user is prompted to select a value."
+  (let* ((p (org-entry-get (point) prop))
+         (lst (when p (split-string-and-unquote p)))
+         (prop-to-remove (or val (completing-read "Remove: " lst)))
+         (lst (delete prop-to-remove lst)))
+    (if lst
+        (org-set-property prop (combine-and-quote-strings lst))
+      (org-delete-property prop))
+    prop-to-remove))
+
+(defun org-roam-property-add (prop val)
+  "Add VAL value to PROP property for the node at point.
+Both, VAL and PROP are strings."
+  (let* ((p (org-entry-get (point) prop))
+         (lst (when p (split-string-and-unquote p)))
+         (lst (if (memq val lst) lst (cons val lst)))
+         (lst (seq-uniq lst)))
+    (org-set-property prop (combine-and-quote-strings lst))
+    val))
+
+(defun org-roam-property-remove (prop &optional val)
+  "Remove VAL value from PROP property for the node at point.
+Both VAL and PROP are strings.
+
+If VAL is not specified, user is prompted to select a value."
+  (let* ((p (org-entry-get (point) prop))
+         (lst (when p (split-string-and-unquote p)))
+         (prop-to-remove (or val (completing-read "Remove: " lst)))
+         (lst (delete prop-to-remove lst)))
+    (if lst
+        (org-set-property prop (combine-and-quote-strings lst))
+      (org-delete-property prop))
+    prop-to-remove))
+
+;;; Refs
+(defun org-roam-org-ref-path-to-keys (path)
+  "Return a list of keys given an org-ref cite: PATH.
+Accounts for both v2 and v3."
+  (cond ((fboundp 'org-ref-parse-cite-path)
+         (mapcar (lambda (cite) (plist-get cite :key))
+                 (plist-get (org-ref-parse-cite-path path) :references)))
+        ((fboundp 'org-ref-split-and-strip-string)
+         (org-ref-split-and-strip-string path))))
+
+;;; Logs
+(defvar org-roam-verbose)
+(defun org-roam-message (format-string &rest args)
+  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
+  (when org-roam-verbose
+    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
 
 ;;; Diagnostics
+;; TODO Update this to also get commit hash
 ;;;###autoload
 (defun org-roam-version (&optional message)
   "Return `org-roam' version.
 Interactively, or when MESSAGE is non-nil, show in the echo area."
   (interactive)
-  (let* ((version
-          (with-temp-buffer
-            (insert-file-contents-literally (locate-library "org-roam.el"))
-            (goto-char (point-min))
-            (save-match-data
-              (if (re-search-forward "\\(?:;; Version: \\([^z-a]*?$\\)\\)" nil nil)
-                  (substring-no-properties (match-string 1))
-                "N/A")))))
+  (let* ((toplib (or load-file-name buffer-file-name))
+         gitdir topdir version)
+    (unless (and toplib (equal (file-name-nondirectory toplib) "org-roam-utils.el"))
+      (setq toplib (locate-library "org-roam-utils.el")))
+    (setq toplib (and toplib (org-roam--straight-chase-links toplib)))
+    (when toplib
+      (setq topdir (file-name-directory toplib)
+            gitdir (expand-file-name ".git" topdir)))
+    (when (file-exists-p gitdir)
+      (setq version
+            (let ((default-directory topdir))
+              (shell-command-to-string "git describe --tags --dirty --always"))))
+    (unless version
+      (setq version (with-temp-buffer
+                      (insert-file-contents-literally (locate-library "org-roam.el"))
+                      (goto-char (point-min))
+                      (save-match-data
+                        (if (re-search-forward "\\(?:;; Version: \\([^z-a]*?$\\)\\)" nil nil)
+                            (substring-no-properties (match-string 1))
+                          "N/A")))))
     (if (or message (called-interactively-p 'interactive))
         (message "%s" version)
       version)))
 
+(defun org-roam--straight-chase-links (filename)
+  "Chase links in FILENAME until a name that is not a link.
+
+This is the same as `file-chase-links', except that it also
+handles fake symlinks that are created by the package manager
+straight.el on Windows.
+
+See <https://github.com/raxod502/straight.el/issues/520>."
+  (when (and (bound-and-true-p straight-symlink-emulation-mode)
+             (fboundp 'straight-chase-emulated-symlink))
+    (when-let ((target (straight-chase-emulated-symlink filename)))
+      (unless (eq target 'broken)
+        (setq filename target))))
+  (file-chase-links filename))
+
 ;;;###autoload
 (defun org-roam-diagnostics ()
   "Collect and print info for `org-roam' issues."
@@ -292,5 +479,6 @@ Interactively, or when MESSAGE is non-nil, show in the echo area."
     (insert (format "- Org: %s\n" (org-version nil 'full)))
     (insert (format "- Org-roam: %s" (org-roam-version)))))
 
+
 (provide 'org-roam-utils)
 ;;; org-roam-utils.el ends here

tests/roam-files/roam-exclude.org

@@ -0,0 +1,7 @@
+:PROPERTIES:
+:ID:       53fadc75-f48e-461e-be06-44a1e88b2abe
+:ROAM_EXCLUDE: t
+:END:
+#+TITLE: Excluded by Org-roam
+
+This node is excluded by declaring ~ROAM_EXCLUDE: t~.

tests/test-org-roam.el

@@ -24,20 +24,43 @@
 (require 'buttercup)
 (require 'org-roam)
 
+(describe "org-roam-list-files"
+  (before-each
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil))
+
+  (it "gets files correctly"
+    (expect (length (org-roam-list-files))
+            :to-equal 3))
+
+  (it "respects org-roam-file-extensions"
+    (setq org-roam-file-extensions '("md"))
+    (expect (length (org-roam-list-files)) :to-equal 1)
+    (setq org-roam-file-extensions '("org" "md"))
+    (expect (length (org-roam-list-files)) :to-equal 4))
+
+  (it "respects org-roam-file-exclude-regexp"
+    (setq org-roam-file-exclude-regexp (regexp-quote "foo.org"))
+    (expect (length (org-roam-list-files)) :to-equal 2)))
+
 (describe "org-roam-db-sync"
   (before-all
     (setq org-roam-directory (expand-file-name "tests/roam-files")
-          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory))
-    (org-roam-setup))
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
 
   (after-all
-    (org-roam-teardown)
+    (org-roam-db--close)
     (delete-file org-roam-db-location))
 
   (it "has the correct number of files"
     (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
             :to-equal
-            2))
+            3))
 
   (it "has the correct number of nodes"
     (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
@@ -47,7 +70,13 @@
   (it "has the correct number of links"
     (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
             :to-equal
-            1)))
+            1))
+
+  (it "respects ROAM_EXCLUDE"
+    ;; The excluded node has ID "53fadc75-f48e-461e-be06-44a1e88b2abe"
+    (expect (mapcar #'car (org-roam-db-query [:select id :from nodes]))
+            :to-have-same-items-as
+            '("884b2341-b7fe-434d-848c-5282c0727861" "440795d0-70c1-4165-993d-aebd5eef7a24"))))
 
 (provide 'test-org-roam)