From 22a66b1b01563ebdc8a904b8e7bbc3a8f0fa0763 Mon Sep 17 00:00:00 2001
From: jethrokuan <jethrokuan95@gmail.com>
Date: Wed, 11 Nov 2020 10:04:42 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20=20@=2016755?=
 =?UTF-8?q?3b8ee45390d113a72eafba75cb56ced5311=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 ...troduction-to-the-Zettelkasten-Method.html | 23 ++---
 manual/Bibliography.html                      |  2 +
 manual/Diagnosing-and-Repairing-Files.html    |  5 +-
 manual/Encryption.html                        |  2 +-
 manual/Fleeting-notes.html                    | 83 +++++++++++++++++++
 manual/Installation-_00281_0029.html          |  8 +-
 manual/Installation.html                      |  2 +-
 .../Installing-from-the-Git-Repository.html   |  2 +-
 manual/{_005f.html => Permanent-notes.html}   | 28 ++++---
 manual/Roam-Protocol.html                     | 13 +--
 manual/The-roam_002dfile-protocol.html        |  2 +-
 manual/The-roam_002dref-protocol.html         |  2 +-
 manual/Titles.html                            |  2 +-
 manual/index.html                             | 25 ++++--
 org-roam.org                                  | 23 +++--
 org-roam.texi                                 | 42 ++++++----
 16 files changed, 189 insertions(+), 75 deletions(-)
 create mode 100644 manual/Fleeting-notes.html
 rename manual/{_005f.html => Permanent-notes.html} (59%)

diff --git a/manual/A-Brief-Introduction-to-the-Zettelkasten-Method.html b/manual/A-Brief-Introduction-to-the-Zettelkasten-Method.html
index aa09578..5a545e1 100644
--- a/manual/A-Brief-Introduction-to-the-Zettelkasten-Method.html
+++ b/manual/A-Brief-Introduction-to-the-Zettelkasten-Method.html
@@ -25,7 +25,7 @@ General Public License for more details.
 <link href="index.html#Top" rel="start" title="Top">
 <link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
 <link href="index.html#Top" rel="up" title="Top">
-<link href="Installation.html#Installation" rel="next" title="Installation">
+<link href="Fleeting-notes.html#Fleeting-notes" rel="next" title="Fleeting notes">
 <link href="Target-Audience.html#Target-Audience" rel="prev" title="Target Audience">
 <style type="text/css">
 <!--
@@ -98,20 +98,13 @@ create new zettels, pre-filling boilerplate content using a powerful templating
 system. Org-roam also facilitates the linking of zettels using Org-mode <code>file:</code>
 links.
 </p>
-<p>A slip-box requires a method of quickly capturing ideas. These are called
-<strong>fleeting notes</strong>: they are simple reminders of information or ideas that will
-need to be processed later on, or trashed. This is typically accomplished using
-<code>org-capture</code> (see <a href="http://www.gnu.org/software/emacs/manual/html_node/org/capture.html#capture">(org)capture</a>), or using Org-roam&rsquo;s daily notes
-functionality (see <a href="Daily_002dnotes.html#Daily_002dnotes">Daily-notes</a>). This provides a central inbox for collecting
-thoughts, to be processed later into permanent notes.
-</p>
-<p>Permanent notes are further split into two categories: <strong>literature notes</strong> and
-<strong>concept notes</strong>. Literature notes can be brief annotations on a particular
-source (e.g. book, website or paper), that you&rsquo;d like to access later on.
-Concept notes require much more care in authoring: they need to be
-self-explanatory and detailed. Org-roam&rsquo;s templating system supports the
-addition of different templates to facilitate the creation of these notes.
-</p>
+<table class="menu" border="0" cellspacing="0">
+<tr><td align="left" valign="top">&bull; <a href="Fleeting-notes.html#Fleeting-notes" accesskey="1">Fleeting notes</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+</td></tr>
+<tr><td align="left" valign="top">&bull; <a href="Permanent-notes.html#Permanent-notes" accesskey="2">Permanent notes</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+</td></tr>
+</table>
+
 <hr>
 <div class="header">
 <p>
diff --git a/manual/Bibliography.html b/manual/Bibliography.html
index 6712ca6..36aea6d 100644
--- a/manual/Bibliography.html
+++ b/manual/Bibliography.html
@@ -76,6 +76,8 @@ tight integration between
 <code>org-roam</code>. This helps you manage your bibliographic notes under
 <code>org-roam</code>.
 </p>
+<p>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 &lsquo;<samp>#+roam_key</samp>&rsquo;.
+</p>
 
 
 
diff --git a/manual/Diagnosing-and-Repairing-Files.html b/manual/Diagnosing-and-Repairing-Files.html
index 506c039..1af4c4e 100644
--- a/manual/Diagnosing-and-Repairing-Files.html
+++ b/manual/Diagnosing-and-Repairing-Files.html
@@ -81,8 +81,9 @@ org-roam-doctor</code>, but note that this may take some time.
 the check only for the current buffer.
 </p></dd></dl>
 
-<p>The checks run are defined in <code>org-roam-doctor--checkers</code>. Each checker is an
-instance of <code>org-roam-doctor-checker</code>. To define a checker, use
+<p>The checks run are defined in <code>org-roam-doctor--checkers</code>. By default, there are checkers for broken links and invalid &lsquo;<samp>#+roam_*</samp>&rsquo; properties.
+</p>
+<p>Each checker is an instance of <code>org-roam-doctor-checker</code>. To define a checker, use
 <code>make-org-roam-doctor-checker</code>. Here is a sample definition:
 </p>
 <div class="lisp">
diff --git a/manual/Encryption.html b/manual/Encryption.html
index 6a99193..e6280bb 100644
--- a/manual/Encryption.html
+++ b/manual/Encryption.html
@@ -79,7 +79,7 @@ cache updates if it requires reading the encrypted file. To reduce the
 number of password prompts, you may wish to cache the password.
 </p>
 <dl>
-<dt><a name="index-org_002droam_002dencrypt_002dfiles"></a>Variable: <strong>org-roam-encrypt-files</strong></dt>
+<dt><a name="index-org_002droam_002dencrypt_002dfiles"></a>User Option: <strong>org-roam-encrypt-files</strong></dt>
 <dd>
 <p>Whether to encrypt new files.  If true, create files with .org.gpg extension.
 </p></dd></dl>
diff --git a/manual/Fleeting-notes.html b/manual/Fleeting-notes.html
new file mode 100644
index 0000000..d521387
--- /dev/null
+++ b/manual/Fleeting-notes.html
@@ -0,0 +1,83 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- 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.
+ -->
+<!-- Created by GNU Texinfo 6.5, http://www.gnu.org/software/texinfo/ -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<title>Fleeting notes (Org-roam User Manual)</title>
+
+<meta name="description" content="Fleeting notes (Org-roam User Manual)">
+<meta name="keywords" content="Fleeting notes (Org-roam User Manual)">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method" rel="up" title="A Brief Introduction to the Zettelkasten Method">
+<link href="Permanent-notes.html#Permanent-notes" rel="next" title="Permanent notes">
+<link href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method" rel="prev" title="A Brief Introduction to the Zettelkasten Method">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="assets/page.css">
+
+
+</head>
+
+<body lang="en">
+<a name="Fleeting-notes"></a>
+<div class="header">
+<p>
+Next: <a href="Permanent-notes.html#Permanent-notes" accesskey="n" rel="next">Permanent notes</a>, Up: <a href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method" accesskey="u" rel="up">A Brief Introduction to the Zettelkasten Method</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<hr>
+<a name="Fleeting-notes-1"></a>
+<h3 class="section">3.1 Fleeting notes</h3>
+
+<p>A slip-box requires a method of quickly capturing ideas. These are called
+<strong>fleeting notes</strong>: they are simple reminders of information or ideas that will
+need to be processed later on, or trashed. This is typically accomplished using
+<code>org-capture</code> (see <a href="http://www.gnu.org/software/emacs/manual/html_node/org/capture.html#capture">(org)capture</a>), or using Org-roam&rsquo;s daily notes
+functionality (see <a href="Daily_002dnotes.html#Daily_002dnotes">Daily-notes</a>). This provides a central inbox for collecting
+thoughts, to be processed later into permanent notes.
+</p>
+
+
+
+</body>
+</html>
diff --git a/manual/Installation-_00281_0029.html b/manual/Installation-_00281_0029.html
index 576b6e6..f5cc6d8 100644
--- a/manual/Installation-_00281_0029.html
+++ b/manual/Installation-_00281_0029.html
@@ -26,7 +26,7 @@ General Public License for more details.
 <link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
 <link href="Roam-Protocol.html#Roam-Protocol" rel="up" title="Roam Protocol">
 <link href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" rel="next" title="The roam-file protocol">
-<link href="_005f.html#g_t_005f" rel="prev" title="_">
+<link href="Roam-Protocol.html#Roam-Protocol" rel="prev" title="Roam Protocol">
 <style type="text/css">
 <!--
 a.summary-letter {text-decoration: none}
@@ -63,11 +63,11 @@ ul.no-bullet {list-style: none}
 <a name="Installation-_00281_0029"></a>
 <div class="header">
 <p>
-Next: <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" accesskey="n" rel="next">The roam-file protocol</a>, Previous: <a href="_005f.html#g_t_005f" accesskey="p" rel="prev">_</a>, Up: <a href="Roam-Protocol.html#Roam-Protocol" accesskey="u" rel="up">Roam Protocol</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+Next: <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" accesskey="n" rel="next">The roam-file protocol</a>, Up: <a href="Roam-Protocol.html#Roam-Protocol" accesskey="u" rel="up">Roam Protocol</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
 </div>
 <hr>
 <a name="Installation-2"></a>
-<h3 class="section">14.2 Installation</h3>
+<h3 class="section">14.1 Installation</h3>
 
 <p>To enable Org-roam&rsquo;s protocol extensions, you have to add the following to your init file:
 </p>
@@ -210,7 +210,7 @@ the default handler instead, run:
 <hr>
 <div class="header">
 <p>
-Next: <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" accesskey="n" rel="next">The roam-file protocol</a>, Previous: <a href="_005f.html#g_t_005f" accesskey="p" rel="prev">_</a>, Up: <a href="Roam-Protocol.html#Roam-Protocol" accesskey="u" rel="up">Roam Protocol</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+Next: <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" accesskey="n" rel="next">The roam-file protocol</a>, Up: <a href="Roam-Protocol.html#Roam-Protocol" accesskey="u" rel="up">Roam Protocol</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
 </div>
 
 
diff --git a/manual/Installation.html b/manual/Installation.html
index 0b2d6b6..c713339 100644
--- a/manual/Installation.html
+++ b/manual/Installation.html
@@ -26,7 +26,7 @@ General Public License for more details.
 <link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
 <link href="index.html#Top" rel="up" title="Top">
 <link href="Installing-from-MELPA.html#Installing-from-MELPA" rel="next" title="Installing from MELPA">
-<link href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method" rel="prev" title="A Brief Introduction to the Zettelkasten Method">
+<link href="Permanent-notes.html#Permanent-notes" rel="prev" title="Permanent notes">
 <style type="text/css">
 <!--
 a.summary-letter {text-decoration: none}
diff --git a/manual/Installing-from-the-Git-Repository.html b/manual/Installing-from-the-Git-Repository.html
index 1a40d8f..9766bba 100644
--- a/manual/Installing-from-the-Git-Repository.html
+++ b/manual/Installing-from-the-Git-Repository.html
@@ -119,7 +119,7 @@ Next: <a href="Post_002dInstallation-Tasks.html#Post_002dInstallation-Tasks" acc
 <div class="lisp">
 <pre class="lisp">(require 'info)
 (add-to-list 'Info-default-directory-list
-         &quot;/path/to/my/info/files&quot;)
+             &quot;/path/to/my/info/files&quot;)
 </pre></div>
 
 <p>You can also use one of the default locations, such as:
diff --git a/manual/_005f.html b/manual/Permanent-notes.html
similarity index 59%
rename from manual/_005f.html
rename to manual/Permanent-notes.html
index 986ee85..2982f06 100644
--- a/manual/_005f.html
+++ b/manual/Permanent-notes.html
@@ -15,18 +15,18 @@ General Public License for more details.
 <!-- Created by GNU Texinfo 6.5, http://www.gnu.org/software/texinfo/ -->
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<title>_ (Org-roam User Manual)</title>
+<title>Permanent notes (Org-roam User Manual)</title>
 
-<meta name="description" content="_ (Org-roam User Manual)">
-<meta name="keywords" content="_ (Org-roam User Manual)">
+<meta name="description" content="Permanent notes (Org-roam User Manual)">
+<meta name="keywords" content="Permanent notes (Org-roam User Manual)">
 <meta name="resource-type" content="document">
 <meta name="distribution" content="global">
 <meta name="Generator" content="makeinfo">
 <link href="index.html#Top" rel="start" title="Top">
 <link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
-<link href="Roam-Protocol.html#Roam-Protocol" rel="up" title="Roam Protocol">
-<link href="Installation-_00281_0029.html#Installation-_00281_0029" rel="next" title="Installation (1)">
-<link href="Roam-Protocol.html#Roam-Protocol" rel="prev" title="Roam Protocol">
+<link href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method" rel="up" title="A Brief Introduction to the Zettelkasten Method">
+<link href="Installation.html#Installation" rel="next" title="Installation">
+<link href="Fleeting-notes.html#Fleeting-notes" rel="prev" title="Fleeting notes">
 <style type="text/css">
 <!--
 a.summary-letter {text-decoration: none}
@@ -60,17 +60,21 @@ ul.no-bullet {list-style: none}
 </head>
 
 <body lang="en">
-<a name="g_t_005f"></a>
+<a name="Permanent-notes"></a>
 <div class="header">
 <p>
-Next: <a href="Installation-_00281_0029.html#Installation-_00281_0029" accesskey="n" rel="next">Installation (1)</a>, Up: <a href="Roam-Protocol.html#Roam-Protocol" accesskey="u" rel="up">Roam Protocol</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+Previous: <a href="Fleeting-notes.html#Fleeting-notes" accesskey="p" rel="prev">Fleeting notes</a>, Up: <a href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method" accesskey="u" rel="up">A Brief Introduction to the Zettelkasten Method</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
 </div>
 <hr>
-<a name="g_t_005f-_003aignore_003a"></a>
-<h3 class="section">14.1 _ :ignore:</h3>
+<a name="Permanent-notes-1"></a>
+<h3 class="section">3.2 Permanent notes</h3>
 
-<p>Org-roam extending <code>org-protocol</code> with 2 protocols: the <code>roam-file</code>
-and <code>roam-ref</code> protocol.
+<p>Permanent notes are further split into two categories: <strong>literature notes</strong> and
+<strong>concept notes</strong>. Literature notes can be brief annotations on a particular
+source (e.g. book, website or paper), that you&rsquo;d like to access later on.
+Concept notes require much more care in authoring: they need to be
+self-explanatory and detailed. Org-roam&rsquo;s templating system supports the
+addition of different templates to facilitate the creation of these notes.
 </p>
 
 
diff --git a/manual/Roam-Protocol.html b/manual/Roam-Protocol.html
index 8a759c4..981e2c3 100644
--- a/manual/Roam-Protocol.html
+++ b/manual/Roam-Protocol.html
@@ -25,7 +25,7 @@ General Public License for more details.
 <link href="index.html#Top" rel="start" title="Top">
 <link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
 <link href="index.html#Top" rel="up" title="Top">
-<link href="_005f.html#g_t_005f" rel="next" title="_">
+<link href="Installation-_00281_0029.html#Installation-_00281_0029" rel="next" title="Installation (1)">
 <link href="Org_002droam-Completion-System.html#Org_002droam-Completion-System" rel="prev" title="Org-roam Completion System">
 <style type="text/css">
 <!--
@@ -69,14 +69,15 @@ Next: <a href="Daily_002dnotes.html#Daily_002dnotes" accesskey="n" rel="next">Da
 <a name="Roam-Protocol-1"></a>
 <h2 class="chapter">14 Roam Protocol</h2>
 
+<p>Org-roam extends <code>org-protocol</code> with 2 protocols: the <code>roam-file</code>
+and <code>roam-ref</code> protocols.
+</p>
 <table class="menu" border="0" cellspacing="0">
-<tr><td align="left" valign="top">&bull; <a href="_005f.html#g_t_005f" accesskey="1">_</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+<tr><td align="left" valign="top">&bull; <a href="Installation-_00281_0029.html#Installation-_00281_0029" accesskey="1">Installation</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
 </td></tr>
-<tr><td align="left" valign="top">&bull; <a href="Installation-_00281_0029.html#Installation-_00281_0029" accesskey="2">Installation</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+<tr><td align="left" valign="top">&bull; <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" accesskey="2">The roam-file protocol</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
 </td></tr>
-<tr><td align="left" valign="top">&bull; <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" accesskey="3">The roam-file protocol</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
-</td></tr>
-<tr><td align="left" valign="top">&bull; <a href="The-roam_002dref-protocol.html#The-roam_002dref-protocol" accesskey="4">The roam-ref protocol</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+<tr><td align="left" valign="top">&bull; <a href="The-roam_002dref-protocol.html#The-roam_002dref-protocol" accesskey="3">The roam-ref protocol</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
 </td></tr>
 </table>
 
diff --git a/manual/The-roam_002dfile-protocol.html b/manual/The-roam_002dfile-protocol.html
index 9b13b4f..9ee5b80 100644
--- a/manual/The-roam_002dfile-protocol.html
+++ b/manual/The-roam_002dfile-protocol.html
@@ -67,7 +67,7 @@ Next: <a href="The-roam_002dref-protocol.html#The-roam_002dref-protocol" accessk
 </div>
 <hr>
 <a name="The-roam_002dfile-protocol-1"></a>
-<h3 class="section">14.3 The roam-file protocol</h3>
+<h3 class="section">14.2 The roam-file protocol</h3>
 
 <p>This is a simple protocol that opens the path specified by the <code>file</code>
 key (e.g. <code>org-protocol://roam-file?file=/tmp/file.org</code>). This is used
diff --git a/manual/The-roam_002dref-protocol.html b/manual/The-roam_002dref-protocol.html
index 24b57dd..c014990 100644
--- a/manual/The-roam_002dref-protocol.html
+++ b/manual/The-roam_002dref-protocol.html
@@ -67,7 +67,7 @@ Previous: <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol" a
 </div>
 <hr>
 <a name="The-roam_002dref-protocol-1"></a>
-<h3 class="section">14.4 The roam-ref protocol</h3>
+<h3 class="section">14.3 The roam-ref protocol</h3>
 
 <p>This protocol finds or creates a new note with a given <code>roam_key</code> (see <a href="Anatomy-of-an-Org_002droam-File.html#Anatomy-of-an-Org_002droam-File">Anatomy of an Org-roam File</a>):
 </p>
diff --git a/manual/Titles.html b/manual/Titles.html
index 4964357..2574c1c 100644
--- a/manual/Titles.html
+++ b/manual/Titles.html
@@ -85,7 +85,7 @@ title extraction methods supported are:
 </li><li> <code>'headline</code>: This extracts the title from the first headline in the Org file
 
 </li><li> <code>'alias</code>: This extracts a list of titles using the <code>#+roam_alias</code> property.
-The aliases are space-delimited, and can be multi-worded using quotes
+The aliases are space-delimited, and can be multi-worded using quotes.
 </li></ul>
 
 <p>Take for example the following org file:
diff --git a/manual/index.html b/manual/index.html
index 861fa2a..334c379 100644
--- a/manual/index.html
+++ b/manual/index.html
@@ -72,7 +72,11 @@ ul.no-bullet {list-style: none}
 <ul class="no-bullet">
   <li><a name="toc-Introduction-1" href="Introduction.html#Introduction">1 Introduction</a></li>
   <li><a name="toc-Target-Audience-1" href="Target-Audience.html#Target-Audience">2 Target Audience</a></li>
-  <li><a name="toc-A-Brief-Introduction-to-the-Zettelkasten-Method-1" href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method">3 A Brief Introduction to the Zettelkasten Method</a></li>
+  <li><a name="toc-A-Brief-Introduction-to-the-Zettelkasten-Method-1" href="A-Brief-Introduction-to-the-Zettelkasten-Method.html#A-Brief-Introduction-to-the-Zettelkasten-Method">3 A Brief Introduction to the Zettelkasten Method</a>
+  <ul class="no-bullet">
+    <li><a name="toc-Fleeting-notes-1" href="Fleeting-notes.html#Fleeting-notes">3.1 Fleeting notes</a></li>
+    <li><a name="toc-Permanent-notes-1" href="Permanent-notes.html#Permanent-notes">3.2 Permanent notes</a></li>
+  </ul></li>
   <li><a name="toc-Installation-1" href="Installation.html#Installation">4 Installation</a>
   <ul class="no-bullet">
     <li><a name="toc-Installing-from-MELPA-1" href="Installing-from-MELPA.html#Installing-from-MELPA">4.1 Installing from MELPA</a></li>
@@ -113,10 +117,9 @@ ul.no-bullet {list-style: none}
   <li><a name="toc-Org_002droam-Completion-System-1" href="Org_002droam-Completion-System.html#Org_002droam-Completion-System">13 Org-roam Completion System</a></li>
   <li><a name="toc-Roam-Protocol-1" href="Roam-Protocol.html#Roam-Protocol">14 Roam Protocol</a>
   <ul class="no-bullet">
-    <li><a name="toc-_005f-_003aignore_003a" href="_005f.html#g_t_005f">14.1 _ :ignore:</a></li>
-    <li><a name="toc-Installation-2" href="Installation-_00281_0029.html#Installation-_00281_0029">14.2 Installation</a></li>
-    <li><a name="toc-The-roam_002dfile-protocol-1" href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol">14.3 The roam-file protocol</a></li>
-    <li><a name="toc-The-roam_002dref-protocol-1" href="The-roam_002dref-protocol.html#The-roam_002dref-protocol">14.4 The roam-ref protocol</a></li>
+    <li><a name="toc-Installation-2" href="Installation-_00281_0029.html#Installation-_00281_0029">14.1 Installation</a></li>
+    <li><a name="toc-The-roam_002dfile-protocol-1" href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol">14.2 The roam-file protocol</a></li>
+    <li><a name="toc-The-roam_002dref-protocol-1" href="The-roam_002dref-protocol.html#The-roam_002dref-protocol">14.3 The roam-ref protocol</a></li>
   </ul></li>
   <li><a name="toc-Daily_002dnotes-1" href="Daily_002dnotes.html#Daily_002dnotes">15 Daily-notes</a>
   <ul class="no-bullet">
@@ -231,6 +234,14 @@ General Public License for more details.
 
 </pre></th></tr><tr><th colspan="3" align="left" valign="top"><pre class="menu-comment">&mdash; The Detailed Node Listing &mdash;
 
+A Brief Introduction to the Zettelkasten Method
+
+</pre></th></tr><tr><td align="left" valign="top">&bull; <a href="Fleeting-notes.html#Fleeting-notes">Fleeting notes</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+</td></tr>
+<tr><td align="left" valign="top">&bull; <a href="Permanent-notes.html#Permanent-notes">Permanent notes</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+</td></tr>
+<tr><th colspan="3" align="left" valign="top"><pre class="menu-comment">
+
 Installation
 
 </pre></th></tr><tr><td align="left" valign="top">&bull; <a href="Installing-from-MELPA.html#Installing-from-MELPA">Installing from MELPA</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
@@ -289,9 +300,7 @@ Graphing
 
 Roam Protocol
 
-</pre></th></tr><tr><td align="left" valign="top">&bull; <a href="_005f.html#g_t_005f">_</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
-</td></tr>
-<tr><td align="left" valign="top">&bull; <a href="Installation-_00281_0029.html#Installation-_00281_0029">Installation</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
+</pre></th></tr><tr><td align="left" valign="top">&bull; <a href="Installation-_00281_0029.html#Installation-_00281_0029">Installation</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
 </td></tr>
 <tr><td align="left" valign="top">&bull; <a href="The-roam_002dfile-protocol.html#The-roam_002dfile-protocol">The roam-file protocol</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
 </td></tr>
diff --git a/org-roam.org b/org-roam.org
index 540fa0d..fc94ac8 100644
--- a/org-roam.org
+++ b/org-roam.org
@@ -12,7 +12,7 @@
 #+texinfo_dir_desc: Rudimentary Roam Replica for Emacs.
 #+subtitle: for version 1.2.2
 
-#+options: H:4 num:3 toc:2 creator:t
+#+options: H:4 num:3 toc:2 creator:t ':t
 #+property: header-args :eval never
 #+texinfo: @noindent
 
@@ -122,6 +122,8 @@ create new zettels, pre-filling boilerplate content using a powerful templating
 system. Org-roam also facilitates the linking of zettels using Org-mode ~file:~
 links.
 
+** Fleeting notes
+
 A slip-box requires a method of 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
@@ -129,6 +131,8 @@ need to be processed later on, or trashed. This is typically accomplished using
 functionality (see [[*Daily-notes][Daily-notes]]). This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.
 
+** Permanent notes
+
 Permanent notes are further split into two categories: *literature notes* and
 *concept notes*. Literature notes can be brief annotations on a particular
 source (e.g. book, website or paper), that you'd like to access later on.
@@ -370,7 +374,7 @@ title extraction methods supported are:
 1. ~'title~: This extracts the title using the file ~#+title~ property
 2. ~'headline~: This extracts the title from the first headline in the Org file
 3. ~'alias~: This extracts a list of titles using the ~#+roam_alias~ property.
-   The aliases are space-delimited, and can be multi-worded using quotes
+   The aliases are space-delimited, and can be multi-worded using quotes.
 
 Take for example the following org file:
 
@@ -731,7 +735,7 @@ 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
+- User Option: org-roam-encrypt-files
 
   Whether to encrypt new files.  If true, create files with .org.gpg extension.
 * Graphing
@@ -847,9 +851,9 @@ commands, set:
 Other options include ~'ido~, and ~'ivy~.
 
 * Roam Protocol
-** _ :ignore:
-Org-roam extending ~org-protocol~ with 2 protocols: the ~roam-file~
-and ~roam-ref~ protocol.
+
+Org-roam extends ~org-protocol~ with 2 protocols: the ~roam-file~
+and ~roam-ref~ protocols.
 
 ** Installation
 
@@ -1149,8 +1153,9 @@ org-roam-doctor~, but note that this may take some time.
   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
+The checks run are defined in ~org-roam-doctor--checkers~. By default, there are checkers for broken links and invalid =#+roam_*= properties.
+
+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:
 
 #+BEGIN_SRC emacs-lisp
@@ -1406,6 +1411,8 @@ tight integration between
 ~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_key=.
+
 **** Spaced Repetition
     :PROPERTIES:
     :CUSTOM_ID: spaced-repetition
diff --git a/org-roam.texi b/org-roam.texi
index f13c9d0..ff235f5 100644
--- a/org-roam.texi
+++ b/org-roam.texi
@@ -89,6 +89,11 @@ General Public License for more details.
 @detailmenu
 --- The Detailed Node Listing ---
 
+A Brief Introduction to the Zettelkasten Method
+
+* Fleeting notes::
+* Permanent notes::
+
 Installation
 
 * Installing from MELPA::
@@ -125,7 +130,6 @@ Graphing
 
 Roam Protocol
 
-* _::
 * Installation: Installation (1). 
 * The roam-file protocol::
 * The roam-ref protocol::
@@ -267,6 +271,14 @@ create new zettels, pre-filling boilerplate content using a powerful templating
 system. Org-roam also facilitates the linking of zettels using Org-mode @code{file:}
 links.
 
+@menu
+* Fleeting notes::
+* Permanent notes::
+@end menu
+
+@node Fleeting notes
+@section Fleeting notes
+
 A slip-box requires a method of quickly capturing ideas. These are called
 @strong{fleeting notes}: they are simple reminders of information or ideas that will
 need to be processed later on, or trashed. This is typically accomplished using
@@ -274,6 +286,9 @@ need to be processed later on, or trashed. This is typically accomplished using
 functionality (see @ref{Daily-notes}). This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.
 
+@node Permanent notes
+@section Permanent notes
+
 Permanent notes are further split into two categories: @strong{literature notes} and
 @strong{concept notes}. Literature notes can be brief annotations on a particular
 source (e.g. book, website or paper), that you'd like to access later on.
@@ -418,7 +433,7 @@ Where @code{/path/to/my/info/files} is the location where you keep info files. T
 @lisp
 (require 'info)
 (add-to-list 'Info-default-directory-list
-         "/path/to/my/info/files")
+             "/path/to/my/info/files")
 @end lisp
 
 You can also use one of the default locations, such as:
@@ -568,7 +583,7 @@ title extraction methods supported are:
 
 @item
 @code{'alias}: This extracts a list of titles using the @code{#+roam_alias} property.
-The aliases are space-delimited, and can be multi-worded using quotes
+The aliases are space-delimited, and can be multi-worded using quotes.
 @end itemize
 
 Take for example the following org file:
@@ -1026,10 +1041,10 @@ 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.
 
-@defvar org-roam-encrypt-files
+@defopt org-roam-encrypt-files
 
 Whether to encrypt new files.  If true, create files with .org.gpg extension.
-@end defvar
+@end defopt
 
 @node Graphing
 @chapter Graphing
@@ -1181,19 +1196,15 @@ Other options include @code{'ido}, and @code{'ivy}.
 @node Roam Protocol
 @chapter Roam Protocol
 
+Org-roam extends @code{org-protocol} with 2 protocols: the @code{roam-file}
+and @code{roam-ref} protocols.
+
 @menu
-* _::
 * Installation: Installation (1). 
 * The roam-file protocol::
 * The roam-ref protocol::
 @end menu
 
-@node _
-@section _ :ignore:
-
-Org-roam extending @code{org-protocol} with 2 protocols: the @code{roam-file}
-and @code{roam-ref} protocol.
-
 @node Installation (1)
 @section Installation
 
@@ -1527,8 +1538,9 @@ Perform a check on Org-roam files to ensure cleanliness. If THIS-BUFFER, run
 the check only for the current buffer.
 @end defun
 
-The checks run are defined in @code{org-roam-doctor--checkers}. Each checker is an
-instance of @code{org-roam-doctor-checker}. To define a checker, use
+The checks run are defined in @code{org-roam-doctor--checkers}. By default, there are checkers for broken links and invalid @samp{#+roam_*} properties.
+
+Each checker is an instance of @code{org-roam-doctor-checker}. To define a checker, use
 @code{make-org-roam-doctor-checker}. Here is a sample definition:
 
 @lisp
@@ -1822,6 +1834,8 @@ tight integration between
 @code{org-roam}. This helps you manage your bibliographic notes under
 @code{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 @samp{#+roam_key}.
+
 @node Spaced Repetition
 @unnumberedsubsubsec Spaced Repetition