     Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@gmail.com>

     You can redistribute this document and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

     This document 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.

Org-roam User Manual
********************

This manual is for Org-roam version 1.1.1.

     Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@gmail.com>

     You can redistribute this document and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

     This document 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.

Introduction
************

Org-roam is a Roam Research (https://roamresearch.com/) replica built around the all-powerful Org-mode (https://orgmode.org/).

Org-roam is a solution for effortless non-hierarchical note-taking with Org-mode. With Org-roam, notes flow naturally, making note-taking fun and easy. Org-roam should also work as a plug-and-play solution for anyone already using Org-mode for their personal wiki.

To understand more about Roam, a collection of links are available in Note-taking Workflows.

Org-roam aims to implement the core features of Roam, leveraging the mature ecosystem around Org-mode where possible. Eventually, we hope to further introduce features enabled by the Emacs ecosystem.

Org-roam provides several benefits over other tooling:

Privacy and Security
     Edit your personal wiki completely offline, entirely in your control. Encrypt your notes with GPG.

Longevity of Plain Text
     Unlike web solutions like Roam research, the notes are first and foremost plain Org-mode files -- Org-roam simply builds up an auxilliary database to give the personal wiki superpowers. Having your notes in plain-text is crucial for the longevity of your wiki. Never have to worry about proprietary web solutions being taken down. Edit your plain-text notes in notepad if all other editors cease to exist

Free and Open Source
     Org-roam is free and open-source, which means that if you feel unhappy with any part of Org-roam, you may choose to extend Org-roam, or open a PR.

Leverages the Org-mode ecosystem
     Over the years, Emacs and Org-mode has developed into a mature system for plain-text organization. Building upon Org-mode already puts Org-roam light-years ahead of many other solutions.

Built on Emacs
     Emacs is also a fantastic interface for editing text, and we can inherit many of the powerful text-navigation and editing packages available to Emacs.

Installation
************

Org-roam can be installed using Emacs' package manager or manually from its development repository.

Installing from MELPA
=====================

Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs' package manager before, you may familiarize yourself with it by reading the documentation in the Emacs manual, see info:emacs#Packages. Then, add one of the archives to package-archives:

  * To use Melpa:

     (require 'package)
     (add-to-list 'package-archives
                  '("melpa" . "http://melpa.org/packages/") t)

  * To use Melpa-Stable:

     (require 'package)
     (add-to-list 'package-archives
                  '("melpa-stable" . "http://stable.melpa.org/packages/") t)

Once you have added your preferred archive, you need to update the local package list using:

     M-x package-refresh-contents RET

Once you have done that, you can install Org-roam and its dependencies using:

     M-x package-install RET org-roam RET

Now see Post-Installation Tasks.

TODO Installing from the Git Repository
=======================================

TODO Post-Installation Tasks
============================

Getting Started
***************

This short tutorial describes the essential commands used in Org-roam, to help you get started.

First, it is important to understand how Org-roam was designed. Org-roam was built to support a workflow that was not possible with vanilla Org-mode. This flow is modelled after the Zettelkasten Method (https://zettelkasten.de/), and many of Roam Research's (https://roamresearch.com) workflows. Org-roam does not magically make note-taking better -- this often requires a radical change in your current note-taking workflow. To understand more about the methods and madness, see Note-taking Workflows.

To begin using Org-roam, one should set the org-roam-directory to the directory containing your notes. For this tutorial, create an empty directory, and set the org-roam-directory:

     (make-directory "~/org-roam")
     (setq org-roam-directory "~/org-roam")

We encourage using a flat hierarchy for storing notes, but some prefer using folders for storing specific kinds of notes (e.g. websites, papers). This is fine; Org-roam searches recursively within org-roam-directory for any notes. Instead of relying on the file hierarchy for any form of categorization, we solely rely on links between files to establish connections between notes.

Next, we need to enable the global minor mode org-roam-mode. This sets up Emacs with several hooks, builds a cache and keeps it consistent. We recommend starting org-roam-mode on startup:

     (add-hook 'after-init-hook 'org-roam-mode)

To build the cache manually, one can run M-x org-roam-db-build-cache. The cache is a sqlite database named org-roam.db, which defaults to residing in the root org-roam-directory. Cache builds may take a while the first time, but is often instantaneous in subsequent runs.

Let us now create our first note. Call M-x org-roam-find-file. This shows a list of titles for notes that reside in org-roam-directory. It should show nothing right now, since there are no notes in the directory. Entering the title of the note you wish to create, and pressing RET should begin the note creation process. This process uses org-capture's templating system, and can be freely customized (see The Templating System). Using the default template, pressing C-c C-c finishes the note capture. Running M-x org-roam-find-file again should show the note you have created, and selecting that entry will bring you to that note.

The crux of Org-roam is making it easy to create notes, and link them together. To link notes together, we call M-x org-roam-insert. This brings up a prompt with a list of title for existing notes. Selecting an existing entry will create and insert a link to the current file. Entering a non-existent title will create a new note with that title. Good usage of Org-roam requires liberally linking files: this facilitates building up a dense knowledge graph of inter-connected notes.

Org-roam provides an interface to view backlinks. It shows backlinks for the currently active Org-roam note, along with some surrounding context. To toggle the visibility of this buffer, call M-x org-roam.

For a visual representation of the notes and their connections, Org-roam also provides graphing capabilities, using Graphviz. It generates graphs with notes as nodes, and links between them as edges. The generated graph can be used to navigate to the files, but this requires some additional setup (see Roam Protocol).

Anatomy of an Org-roam File
***************************

The bulk of Org-roam's functionality is built on top of vanilla Org-mode. However, to support additional functionality, Org-roam adds several Org-roam-specific keywords. These functionality are not crucial to effective use of Org-roam.

File Aliases
============

Suppose you want a note to be referred to by different names (e.g. ``World War 2'', ``WWII''). You may specify such aliases using the #+ROAM_ALIAS attribute:

     #+TITLE: World War 2
     #+ROAM_ALIAS: "WWII" "World War II"

File Refs
=========

Refs are unique identifiers for files. Each note can only have 1 ref. For example, a note for a website may contain a ref:

     #+TITLE: Google
     #+ROAM_KEY: https://www.google.com/

These keys come in useful for when taking website notes, using the roam-ref protocol (see Roam Protocol).

Alternatively, add a ref for notes for a specific paper, using its org-ref (https://github.com/jkitchin/org-ref) citation key:

     #+TITLE: Neural Ordinary Differential Equations
     #+ROAM_KEY: cite:chen18_neural_ordin_differ_equat

The backlinks buffer will show any cites of this key: e.g.

Figure: org-ref-citelink

The Templating System
*********************

Rather than creating blank files on org-roam-insert and org-roam-find-file, it may be desirable to prefill the file with templated content. This may include:

  * Time of creation

  * File it was created from

  * Clipboard content

  * Any other data you may want to input manually

This requires a complex template insertion system. Fortunately, Org ships with a powerful one: org-capture. However, org-capture was not designed for such use. Org-roam abuses org-capture, extending its syntax. To first understand how org-roam's templating system works, it may be useful to look into basic usage of org-capture.

Org-roam's templates can be customized by modifying the variable org-roam-capture-templates.

Template Walkthrough
====================

To demonstrate the additions made to org-capture templates. Here, we walkthrough the default template, reproduced below.

     ("d" "default" plain (function org-roam--capture-get-point)
          "%?"
          :file-name "%<%Y%m%d%H%M%S>-${slug}"
          :head "#+TITLE: ${title}\n"
          :unnarrowed t)

 1. The template has short key "d". If you have only one template, org-roam automatically chooses this template for you.

 2. The template is given a description of "default".

 3. plain text is inserted. Other options include Org headings via entry.

 4. (function org-roam--capture-get-point) should not be changed.

 5. "%?" is the template inserted on each call to org-roam-capture--capture. This template means don't insert any content, but place the cursor here.

 6. :file-name is the file-name template for a new note, if it doesn't yet exist. This creates a file at path that looks like /path/to/org-roam-directory/20200213032037-foo.org.

 7. :head contains the initial template to be inserted (once only), at the beginning of the file. Here, the title global attribute is inserted.

 8. :unnarrowed t tells org-capture to show the contents for the whole file, rather than narrowing to just the entry.

Other options you may want to learn about include :immediate-finish.

Org-roam Template Expansion
===========================

Org-roam's template definitions also extend org-capture's template syntax, to allow prefilling of strings. We have seen a glimpse of this in Template Walkthrough.

In org-roam templates, the ${var} syntax allows for the expansion of variables, stored in org-roam-capture--info. For example, during org-roam-insert, the user is prompted for a title. Upon entering a non-existent title, the title key in org-roam-capture--info is set to the provided title. ${title} is then expanded into the provided title during the org-capture process. Any variables that do not contain strings, are prompted for values using completing-read.

After doing this expansion, the org-capture's template expansion system is used to fill up the rest of the template. You may read up more on this on org-capture's documentation page (https://orgmode.org/manual/Template-expansion.html#Template-expansion).

To illustrate this dual expansion process, take for example the template string: "%<%Y%m%d%H%M%S>-${title}", with the title "Foo". The template is first expanded into %<%Y%m%d%H%M%S>-Foo. Then org-capture expands %<%Y%m%d%H%M%S> with timestamp: e.g. 20200213032037-Foo.

All of the flexibility afforded by Emacs and Org-mode are available. For example, if you want to encode a UTC timestamp in the filename, you can take advantage of org-mode's %(EXP) template expansion to call format-time-string directly to provide its third argument to specify UTC.

     ("d" "default" plain (function org-roam--capture-get-point)
          "%?"
          :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--${slug}\" (current-time) t)"
          :head "#+TITLE: ${title}\n"
          :unnarrowed t)

Concepts and Configuration
**************************

The number of configuration options is deliberately kept small, to keep the Org-roam codebase manageable. However, we attempt to accommodate as many usage styles as possible.

All of Org-roam's customization options can be viewed via M-x customize-group org-roam.

Directories and Files
=====================

This section concerns the placement and creation of files.

  * Variable: org-roam-directory

     This is the default path to Org-roam files. All Org files, at any level of nesting, are considered part of the Org-roam.

  * Variable: org-roam-db-location

     Location of the Org-roam database. If this is non-nil, the Org-roam sqlite database is saved here.

     It is the user’s responsibility to set this correctly, especially when used with multiple Org-roam instances.

The Org-roam Buffer
===================

The Org-roam buffer displays backlinks for the currently active Org-roam note.

  * User Option: org-roam-buffer

     The name of the org-roam buffer. Defaults to *org-roam*.

  * User Option: org-roam-buffer-position

     The position of the Org-roam buffer side window. Valid values are 'left, 'right, 'top, 'bottom.

  * User Option: org-roam-buffer-width

     Width of org-roam-buffer. Has an effect only if org-roam-buffer-position is 'left or 'right.

  * User Option: org-roam-buffer-height

     Height of org-roam-buffer. Has an effect only if org-roam-buffer-position is 'top or 'bottom.

  * User Option: org-roam-buffer-no-delete-other-windows

     The no-delete-window parameter for the org-roam buffer. Setting it to 't prevents the window from being deleted when calling delete-other-windows.

Org-roam Links
==============

Org-roam links are regular file: links in Org-mode. By default, links are inserted with the title as the link description with org-roam-insert.

  * User Option: org-roam-link-title-format

     To distinguish between org-roam links and regular links, one may choose to use special indicators for Org-roam links. Defaults to "%s".

     If your version of Org is at least 9.2, consider styling the link differently, by customizing the org-roam-link, and org-roam-link-current faces.

Org-roam Files
==============

Org-roam files are created and prefilled using Org-roam's templating system. The templating system is customizable (see The Templating System).

Navigating Around
*****************

Index File
==========

As your collection grows, you might want to create an index where you keep links to your main files.

In Org-roam, you can define the path to your index file by setting org-roam-index-file.

  * Variable: org-roam-index-file

     Path to the Org-roam index file.

     The path can be a string or a function. If it is a string, it should be the path (absolute or relative to org-roam-directory) to the index file. If it is is a function, the function should return the path to the index file. Otherwise, the index is assumed to be a note in org-roam-index whose title is "Index".

  * Function: org-roam-find-index

     Opens the Index file in the current org-roam-directory.

Encryption
**********

One may wish to keep private, encrypted files. Org-roam supports encryption (via GPG), which can be enabled for all new files by setting org-roam-encrypt-files to t. When enabled, new files are created with the .org.gpg extension and decryption are handled automatically by EasyPG.

Note that Emacs will prompt for a password for encrypted files during cache updates if it requires reading the encrypted file. To reduce the number of password prompts, you may wish to cache the password.

  * Variable: org-roam-encrypt-files

     Whether to encrypt new files.  If true, create files with .org.gpg extension.

Graphing
********

Org-roam provides graphing capabilities to explore interconnections between notes. This is done by performing SQL queries and generating images using Graphviz (https://graphviz.org/). The graph can also be navigated: see Roam Protocol.

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

  * Function: org-roam-graph & optional arg file node-query

     Build and possibly display a graph for FILE from NODE-QUERY. If FILE is nil, default to current buffer’s file name. ARG may be any of the following values:

       * nil       show the graph.

       * C-u       show the graph for FILE.

       * C-u N     show the graph for FILE limiting nodes to N steps.

       * C-u C-u   build the graph.

       * C-u -     build the graph for FILE.

       * C-u -N    build the graph for FILE limiting nodes to N steps.

  * User Option: org-roam-graph-executable

     Path to the graphing executable (in this case, Graphviz). Set this if Org-roam is unable to find the Graphviz executable on your system.

     You may also choose to use neato in place of dot, which generates a more compact graph layout.

  * User Option: org-roam-graph-viewer

     Org-roam defaults to using Firefox (located on PATH) to view the SVG, but you may choose to set it to:

      1. A string, which is a path to the program used

      2. a function accepting a single argument: the graph file path.

     nil uses view-file to view the graph.

Graph Options
=============

Graphviz provides many options for customizing the graph output, and Org-roam supports some of them. See https://graphviz.gitlab.io/_pages/doc/info/attrs.html for customizable options.

  * User Option: org-roam-graph-extra-config

     Extra options passed to graphviz for the digraph (The ``G'' attributes). Example: '=(("rankdir" . "LR"))

  * User Option: org-roam-graph-node-extra-config

     Extra options for nodes in the graphviz output (The ``N'' attributes). Example: '(("color" . "skyblue"))

  * User Option: org-roam-graph-edge-extra-config

     Extra options for edges in the graphviz output (The ``E'' attributes). Example: '(("dir" . "back"))

  * User Option: org-roam-graph-edge-cites-extra-config

     Extra options for citation edges in the graphviz output. Example: '(("color" . "red"))

Excluding Nodes and Edges
=========================

One may want to exclude certain files to declutter the graph.

  * User Option: org-roam-graph-exclude-matcher

     Matcher for excluding nodes from the generated graph. Any nodes and links for file paths matching this string is excluded from the graph.

     If value is a string, the string is the only matcher.

     If value is a list, all file paths matching any of the strings are excluded.

     (setq org-roam-graph-exclude-matcher '("private" "dailies"))

This setting excludes all files whose path contain ``private'' or ``dailies''.

Org-roam Completion System
**************************

Org-roam offers completion when choosing note titles etc. The completion system is configurable. The default setting,

     (setq org-roam-completion-system 'default)

uses Emacs' standard completing-read. If you prefer Helm (https://emacs-helm.github.io/helm/), use

     (setq org-roam-completion-system 'helm)

Other options include 'ido, and 'ivy.

Roam Protocol
*************

Org-roam extending org-protocol with 2 protocols: the roam-file and roam-ref protocol.

Installation
============

To enable Org-roam's protocol extensions, you have to add the following to your init file:

     (require 'org-roam-protocol)

The instructions for setting up org-protocol= are reproduced below.

We will also need to create a desktop application for emacsclient. The instructions for various platforms are shown below.

For Linux users, create a desktop application in ~/.local/share/applications/org-protocol.desktop:

     [Desktop Entry]
     Name=Org-Protocol
     Exec=emacsclient %u
     Icon=emacs-icon
     Type=Application
     Terminal=false
     MimeType=x-scheme-handler/org-protocol

Associate org-protocol:// links with the desktop application by running in your shell:

     xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol

To disable the ``confirm'' prompt in Chrome, you can also make Chrome show a checkbox to tick, so that the Org-Protocol Client app will be used without confirmation. To do this, run in a shell:

     sudo mkdir -p /etc/opt/chrome/policies/managed/
     sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
     {
       "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
     }
     EOF
     sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json

and then restart Chrome (for example, by navigating to <chrome://restart>) to make the new policy take effect.

See here (https://www.chromium.org/administrators/linux-quick-start) for more info on the /etc/opt/chrome/policies/managed directory and here (https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox) for information on the ExternalProtocolDialogShowAlwaysOpenCheckbox policy.

For MacOS, one solution is to use Platypus (https://github.com/sveinbjornt/Platypus). Here are the instructions for setting up with Platypus and Chrome:

 1. Install and launch Platypus (with Homebrew (https://brew.sh/)):

     brew cask install platypus

 1. Create a script launch_emacs.sh:

     #!/usr/bin/env bash
     /usr/local/bin/emacsclient --no-wait $1

 1. Create a Platypus app with the following settings:

     | Setting                        | Value                     |
     |--------------------------------+---------------------------|
     | App Name                       | "OrgProtocol"             |
     | Script Type                    | "env" · "/usr/bin/env"    |
     | Script Path                    | "path/to/launch-emacs.sh" |
     | Interface                      | None                      |
     | Accept dropped items           | true                      |
     | Remain running after execution | false                     |

Inside Settings:

     | Setting                        | Value          |
     |--------------------------------+----------------|
     | Accept dropped files           | true           |
     | Register as URI scheme handler | true           |
     | Protocol                       | "org-protocol" |

To disable the ``confirm'' prompt in Chrome, you can also make Chrome show a checkbox to tick, so that the OrgProtocol app will be used without confirmation. To do this, run in a shell:

     defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true

If you're using Emacs Mac Port (https://github.com/railwaycat/homebrew-emacsmacport), it registered its `Emacs.app` as the default handler for the URL scheme `org-protocol`. To make OrgProtocol.app the default handler instead, run:

     defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
     '{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'

Then restart your computer.

The roam-file protocol
======================

This is a simple protocol that opens the path specified by the file key (e.g. org-protocol://roam-file?file=/tmp/file.org). This is used in the generated graph.

The roam-ref Protocol
=====================

This protocol finds or creates a new note with a given ROAM_KEY (see Anatomy of an Org-roam File):

To use this, create a Firefox bookmarklet as follows:

     javascript:location.href =
     'org-protocol://roam-ref?template=r&ref='
     + encodeURIComponent(location.href)
     + '&title='
     + encodeURIComponent(document.title)

or as a keybinding in qutebrowser, adding the following to the autoconfig.yml file:

     settings:
       bindings.commands:
         global:
           normal:
             gc: open javascript:void(location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title))

where template is the template key for a template in org-roam-capture-ref-templates (see The Templating System). These templates should contain a #+ROAM_KEY: ${ref} in it.

Diagnosing and Repairing Files
******************************

Org-roam provides a utility for diagnosing and repairing problematic files via org-roam-doctor. By default, org-roam-doctor runs the check across all Org-roam files, and this can take some time. To run the check only for the current file, run C-u M-x org-roam-doctor.

  * Function: org-roam-doctor &optional this-buffer

     Perform a check on Org-roam files to ensure cleanliness. If THIS-BUFFER, run the check only for the current buffer.

The checks run are defined in org-roam-doctor--checkers. Each checker is an instance of org-roam-doctor-checker. To define a checker, use make-org-roam-doctor-checker. Here is a sample definition:

     (make-org-roam-doctor-checker
         :name 'org-roam-doctor-broken-links
         :description "Fix broken links."
         :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
                    ("r" . ("Replace link" . org-roam-doctor--replace-link))
                    ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))

The :name property is the name of the function run. The function takes in the Org parse tree, and returns a list of (point error-message). :description is a short description of what the checker does. :actions is an alist containing elements of the form (char . (prompt . function)). These actions are defined per checker, to perform autofixes for the errors. For each error detected, org-roam-doctor will move the point to the current error, and pop-up a help window displaying the error message, as well as the list of actions that can be taken provided in :actions.

Appendix
********

Note-taking Workflows
=====================

Books

       * How To Take Smart Notes (https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes)

Articles

       * The Zettelkasten Method - LessWrong 2.0 (https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1)

       * Building a Second Brain in Roam...And Why You Might Want To : RoamResearch (https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might)

       * Roam Research: Why I Love It and How I Use It - Nat Eliason (https://www.nateliason.com/blog/roam)

       * Adam Keesling's Twitter Thread (https://twitter.com/adam_keesling/status/1196864424725774336?s=20)

       * How To Take Smart Notes With Org-mode · Jethro Kuan (https://blog.jethro.dev/posts/how_to_take_smart_notes_org/)

Threads

       * Ask HN: How to Take Good Notes (https://news.ycombinator.com/item?id=22473209)

Videos

       * How to Use Roam to Outline a New Article in Under 20 Minutes (https://www.youtube.com/watch?v=RvWic15iXjk)

Ecosystem
=========

A number of packages work well combined with Org-Roam:

Deft
----

Deft (https://jblevins.org/projects/deft/) provides a nice interface for browsing and filtering org-roam notes.

     (use-package deft
       :after org
       :bind
       ("C-c n d" . deft)
       :custom
       (deft-recursive t)
       (deft-use-filter-string-for-filename t)
       (deft-default-extension "org")
       (deft-directory "/path/to/org-roam-files/"))

If the title of the Org file is not the first line, you might not get nice titles. You may choose to patch this to use org-roam's functionality. Here I'm using el-patch (https://github.com/raxod502/el-patch):

     (use-package el-patch
       :straight (:host github
                        :repo "raxod502/el-patch"
                        :branch "develop"))

     (eval-when-compile
       (require 'el-patch))

     (use-package deft
       ;; same as above...
       :config/el-patch
       (defun deft-parse-title (file contents)
         "Parse the given FILE and CONTENTS and determine the title.
     If `deft-use-filename-as-title' is nil, the title is taken to
     be the first non-empty line of the FILE.  Else the base name of the FILE is
     used as title."
         (el-patch-swap (if deft-use-filename-as-title
                            (deft-base-filename file)
                          (let ((begin (string-match "^.+$" contents)))
                            (if begin
                                (funcall deft-parse-title-function
                                         (substring contents begin (match-end 0))))))
                        (org-roam--get-title-or-slug file))))

The Deft interface can slow down quickly when the number of files get huge. Notdeft (https://github.com/hasu/notdeft) is a fork of Deft that uses an external search engine and indexer.

Org-journal
-----------

Org-journal (https://github.com/bastibe/org-journal) is a more powerful alternative to the simple function org-roam-dailies-today. It provides better journaling capabilities, and a nice calendar interface to see all dated entries.

     (use-package org-journal
       :bind
       ("C-c n j" . org-journal-new-entry)
       :custom
       (org-journal-date-prefix "#+TITLE: ")
       (org-journal-file-format "%Y-%m-%d.org")
       (org-journal-dir "/path/to/org-roam-files/")
       (org-journal-date-format "%A, %d %B %Y"))

Note-taking Add-ons
-------------------

These are some plugins that make note-taking in Org-mode more enjoyable.

Org-download
............

Org-download (https://github.com/abo-abo/org-download) lets you screenshot and yank images from the web into your notes:

Figure: org-download

     (use-package org-download
       :after org
       :bind
       (:map org-mode-map
             (("s-Y" . org-download-screenshot)
              ("s-y" . org-download-yank))))

mathpix.el
..........

mathpix.el (https://github.com/jethrokuan/mathpix.el) uses Mathpix's (https://mathpix.com/) API to convert clips into latex equations:

Figure: mathpix

     (use-package mathpix.el
       :straight (:host github :repo "jethrokuan/mathpix.el")
       :custom ((mathpix-app-id "app-id")
                (mathpix-app-key "app-key"))
       :bind
       ("C-x m" . mathpix-screenshot))

Org-noter / Interleave
......................

Org-noter (https://github.com/weirdNox/org-noter) and Interleave (https://github.com/rudolfochrist/interleave) are both projects that allow synchronised annotation of documents (PDF, EPUB etc.) within Org-mode.

Bibliography
............

org-roam-bibtex (https://github.com/zaeph/org-roam-bibtex) offers tight integration between org-ref (https://github.com/jkitchin/org-ref), helm-bibtex (https://github.com/tmalsburg/helm-bibtex) and org-roam. This helps you manage your bibliographic notes under org-roam.

Spaced Repetition
.................

Org-fc (https://github.com/l3kn/org-fc/) is a spaced repetition system that scales well with a large number of files. Other alternatives include org-drill (https://orgmode.org/worg/org-contrib/org-drill.html), and pamparam (https://github.com/abo-abo/pamparam).

FAQ
***

How do I have more than one Org-roam directory?
===============================================

Emacs supports directory-local variables, allowing the value of org-roam-directory to be different in different directories. It does this by checking for a file named .dir-locals.el.

To add support for multiple directories, override the org-roam-directory variable using directory-local variables. This is what .dir-locals.el may contain:

     ((nil . ((org-roam-directory . "/path/to/here/"))))

All files within that directory will be treated as their own separate set of Org-roam files. Remember to run org-roam-db-build-cache from a file within that directory, at least once.

Emacs 28.0.50 (Org mode 9.4)