From aea20f16f57988e026f818c948b5d05f23c738b2 Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Wed, 13 May 2015 22:55:36 -0400
Subject: [PATCH] updating html for 5.3 release, May 13

---
 00-intro.html      |  2 +-
 01-filedir.html    | 34 +++++++++++++++++++---------------
 02-create.html     | 23 ++++++++++++-----------
 03-pipefilter.html | 25 +++++++++++++------------
 04-loop.html       | 22 +++++++++++-----------
 05-script.html     | 20 ++++++++++----------
 06-find.html       | 21 +++++++++++----------
 discussion.html    |  2 +-
 index.html         |  6 +++---
 reference.html     |  2 +-
 10 files changed, 82 insertions(+), 75 deletions(-)

diff --git a/00-intro.html b/00-intro.html
index 0c83de348..2c2192136 100644
--- a/00-intro.html
+++ b/00-intro.html
@@ -30,7 +30,7 @@ <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Introducing the Shell</h2>
 <section class="objectives panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
+<h2 id="learning-objectives"><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
 </div>
 <div class="panel-body">
 <ul>
diff --git a/01-filedir.html b/01-filedir.html
index 90c4b8621..1d1476b08 100644
--- a/01-filedir.html
+++ b/01-filedir.html
@@ -30,7 +30,7 @@ <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Files and Directories</h2>
 <section class="objectives panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
+<h2 id="learning-objectives"><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
 </div>
 <div class="panel-body">
 <ul>
@@ -62,7 +62,7 @@ <h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2
 <pre class="output"><code>/Users/nelle</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Home directory</h2>
+<h2 id="home-directory"><span class="glyphicon glyphicon-pushpin"></span>Home directory</h2>
 </div>
 <div class="panel-body">
 <p>The home directory path will look different on different operating systems. On Linux it will look like <code>/home/nelle</code>, and on Windows it will be similar to <code>C:\Documents and Settings\nelle</code>. Note that it may look slightly different for different versions of Windows.</p>
@@ -70,7 +70,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Home directory</h2>
 </aside>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Alphabet Soup</h2>
+<h2 id="alphabet-soup"><span class="glyphicon glyphicon-pushpin"></span>Alphabet Soup</h2>
 </div>
 <div class="panel-body">
 <p>If the command to find out who we are is <code>whoami</code>, the command to find out where we are ought to be called <code>whereami</code>, so why is it <code>pwd</code> instead? The usual answer is that in the early 1970s, when Unix was first being developed, every keystroke counted: the devices of the day were slow, and backspacing on a teletype was so painful that cutting the number of keystrokes in order to cut the number of typing mistakes was actually a win for usability. The reality is that commands were added to Unix one by one, without any master plan, by people who were immersed in its jargon. The result is as inconsistent as the roolz uv Inglish speling, but we’re stuck with it now.</p>
@@ -79,12 +79,14 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Alphabet Soup</h2>
 <p>To understand what a “home directory” is, let’s have a look at how the file system as a whole is organized. At the top is the <strong>root directory</strong> that holds everything else. We refer to it using a slash character <code>/</code> on its own; this is the leading slash in <code>/Users/nelle</code>.</p>
 <p>Inside that directory are several other directories: <code>bin</code> (which is where some built-in programs are stored), <code>data</code> (for miscellaneous data files), <code>users</code> (where users’ personal directories are located), <code>tmp</code> (for temporary files that don’t need to be stored long-term), and so on:</p>
 <div class="figure">
-<img src="fig/filesystem.svg" alt="The File System" /><p class="caption">The File System</p>
+<img src="fig/filesystem.svg" alt="The File System" />
+<p class="caption">The File System</p>
 </div>
 <p>We know that our current working directory <code>/Users/nelle</code> is stored inside <code>/Users</code> because <code>/Users</code> is the first part of its name. Similarly, we know that <code>/Users</code> is stored inside the root directory <code>/</code> because its name begins with <code>/</code>.</p>
 <p>Underneath <code>/Users</code>, we find one directory for each user with an account on this machine. The Mummy’s files are stored in <code>/Users/imhotep</code>, Wolfman’s in <code>/Users/larry</code>, and ours in <code>/Users/nelle</code>, which is why <code>nelle</code> is the last part of the directory’s name.</p>
 <div class="figure">
-<img src="fig/home-directories.svg" alt="Home Directories" /><p class="caption">Home Directories</p>
+<img src="fig/home-directories.svg" alt="Home Directories" />
+<p class="caption">Home Directories</p>
 </div>
 <blockquote>
 <p>Notice that there are two meanings for the <code>/</code> character. When it appears at the front of a file or directory name, it refers to the root directory. When it appears <em>inside</em> a name, it’s just a separator.</p>
@@ -95,7 +97,8 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Alphabet Soup</h2>
 data       north-pacific-gyre  solar.pdf
 Desktop    notes.txt           writing</code></pre>
 <div class="figure">
-<img src="fig/homedir.svg" alt="Nelle’s Home Directory" /><p class="caption">Nelle’s Home Directory</p>
+<img src="fig/homedir.svg" alt="Nelle’s Home Directory" />
+<p class="caption">Nelle’s Home Directory</p>
 </div>
 <p><code>ls</code> prints the names of the files and directories in the current directory in alphabetical order, arranged neatly into columns. We can make its output more comprehensible by using the <strong>flag</strong> <code>-F</code>, which tells <code>ls</code> to add a trailing <code>/</code> to the names of directories:</p>
 <pre class="sourceCode bash"><code class="sourceCode bash">$ <span class="kw">ls</span> -F</code></pre>
@@ -105,7 +108,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Alphabet Soup</h2>
 <p>Here, we can see that <code>/Users/nelle</code> contains six <strong>sub-directories</strong>. The names that don’t have trailing slashes, like <code>notes.txt</code>, <code>pizza.cfg</code>, and <code>solar.pdf</code>, are plain old files. And note that there is a space between <code>ls</code> and <code>-F</code>: without it, the shell thinks we’re trying to run a command called <code>ls-F</code>, which doesn’t exist.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>What’s In A Name?</h2>
+<h2 id="whats-in-a-name"><span class="glyphicon glyphicon-pushpin"></span>What’s In A Name?</h2>
 </div>
 <div class="panel-body">
 <p>You may have noticed that all of Nelle’s files’ names are “something dot something”. This is just a convention: we can call a file <code>mythesis</code> or almost anything else we want. However, most people use two-part names most of the time to help them (and their programs) tell different kinds of files apart. The second part of such a name is called the <strong>filename extension</strong>, and indicates what type of data the file holds: <code>.txt</code> signals a plain text file, <code>.pdf</code> indicates a PDF document, <code>.cfg</code> is a configuration file full of parameters for some program or other, and so on.</p>
@@ -121,7 +124,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>What’s In A Name?</h2>
 <p>Notice, by the way that we spelled the directory name <code>data</code>. It doesn’t have a trailing slash: that’s added to directory names by <code>ls</code> when we use the <code>-F</code> flag to help us tell things apart. And it doesn’t begin with a slash because it’s a <strong>relative path</strong>, i.e., it tells <code>ls</code> how to find something from where we are, rather than from the root of the file system.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Parameters vs. Arguments</h2>
+<h2 id="parameters-vs.arguments"><span class="glyphicon glyphicon-pushpin"></span>Parameters vs. Arguments</h2>
 </div>
 <div class="panel-body">
 <p>According to <a href="https://en.wikipedia.org/wiki/Parameter_(computer_programming)#Parameters_and_arguments">Wikipedia</a>, the terms argument and <strong>parameter</strong> mean slightly different things. In practice, however, most people use them interchangeably or inconsistently, so we will too.</p>
@@ -165,13 +168,13 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Parameters vs. Arguments</
 <p><code>-a</code> stands for “show all”; it forces <code>ls</code> to show us file and directory names that begin with <code>.</code>, such as <code>..</code> (which, if we’re in <code>/Users/nelle</code>, refers to the <code>/Users</code> directory). As you can see, it also displays another special directory that’s just called <code>.</code>, which means “the current working directory”. It may seem redundant to have a name for it, but we’ll see some uses for it soon. Finally, we also see a file called <code>.bash_profile</code>. This file usually contains settings to customize the shell (terminal). For this lesson material it does not contain any settings. There may also be similar files called <code>.bashrc</code> or <code>.bash_login</code>. The <code>.</code> prefix is used to prevent these configuration files from cluttering the terminal when a standard <code>ls</code> command is used.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Orthogonality</h2>
+<h2 id="orthogonality"><span class="glyphicon glyphicon-pushpin"></span>Orthogonality</h2>
 </div>
 <div class="panel-body">
 <p>The special names <code>.</code> and <code>..</code> don’t belong to <code>ls</code>; they are interpreted the same way by every program. For example, if we are in <code>/Users/nelle/data</code>, the command <code>ls ..</code> will give us a listing of <code>/Users/nelle</code>. When the meanings of the parts are the same no matter how they’re combined, programmers say they are <strong>orthogonal</strong>: Orthogonal systems tend to be easier for people to learn because there are fewer special cases and exceptions to keep track of.</p>
 </div>
 </aside>
-<h3 id="nelles-pipeline-organizing-files">Nelle’s Pipeline: Organizing Files</h3>
+<h2 id="nelles-pipeline-organizing-files">Nelle’s Pipeline: Organizing Files</h2>
 <p>Knowing just this much about files and directories, Nelle is ready to organize the files that the protein assay machine will create. First, she creates a directory called <code>north-pacific-gyre</code> (to remind herself where the data came from). Inside that, she creates a directory called <code>2012-07-03</code>, which is the date she started processing the samples. She used to use names like <code>conference-paper</code> and <code>revised-results</code>, but she found them hard to understand after a couple of years. (The final straw was when she found herself creating a directory called <code>revised-revised-results-3</code>.)</p>
 <blockquote>
 <p>Nelle names her directories “year-month-day”, with leading zeroes for months and days, because the shell displays file and directory names in alphabetical order. If she used month names, December would come before July; if she didn’t use leading zeroes, November (‘11’) would come before July (‘7’).</p>
@@ -185,11 +188,12 @@ <h3 id="nelles-pipeline-organizing-files">Nelle’s Pipeline: Organizing Files</
 <pre class="sourceCode bash"><code class="sourceCode bash">$ <span class="kw">ls</span> north-pacific-gyre/</code></pre>
 <p>If she presses tab again, Bash will add <code>2012-07-03/</code> to the command, since it’s the only possible completion. Pressing tab again does nothing, since there are 1520 possibilities; pressing tab twice brings up a list of all the files, and so on. This is called <strong>tab completion</strong>, and we will see it in many other tools as we go on.</p>
 <div class="figure">
-<img src="fig/filesystem-challenge.svg" alt="File System for Challange Questions" /><p class="caption">File System for Challange Questions</p>
+<img src="fig/filesystem-challenge.svg" alt="File System for Challange Questions" />
+<p class="caption">File System for Challange Questions</p>
 </div>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Relative path resolution</h2>
+<h2 id="relative-path-resolution"><span class="glyphicon glyphicon-pencil"></span>Relative path resolution</h2>
 </div>
 <div class="panel-body">
 <p>If <code>pwd</code> displays <code>/Users/thing</code>, what will <code>ls ../backup</code> display?</p>
@@ -203,7 +207,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Relative path resolution</h2
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span><code>ls</code> reading comprehension</h2>
+<h2 id="ls-reading-comprehension"><span class="glyphicon glyphicon-pencil"></span><code>ls</code> reading comprehension</h2>
 </div>
 <div class="panel-body">
 <p>If <code>pwd</code> displays <code>/Users/backup</code>, and <code>-r</code> tells <code>ls</code> to display things in reverse order, what command will display:</p>
@@ -218,7 +222,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span><code>ls</code> reading comp
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Default <code>cd</code> action</h2>
+<h2 id="default-cd-action"><span class="glyphicon glyphicon-pencil"></span>Default <code>cd</code> action</h2>
 </div>
 <div class="panel-body">
 <p>What does the command <code>cd</code> without a directory name do?</p>
@@ -232,7 +236,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Default <code>cd</code> acti
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Exploring more <code>ls</code> arguments</h2>
+<h2 id="exploring-more-ls-arguments"><span class="glyphicon glyphicon-pencil"></span>Exploring more <code>ls</code> arguments</h2>
 </div>
 <div class="panel-body">
 <p>What does the command <code>ls</code> do when used with the <code>-s</code> and <code>-h</code> arguments?</p>
diff --git a/02-create.html b/02-create.html
index 885476464..18f137a62 100644
--- a/02-create.html
+++ b/02-create.html
@@ -30,7 +30,7 @@ <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Creating Things</h2>
 <section class="objectives panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
+<h2 id="learning-objectives"><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
 </div>
 <div class="panel-body">
 <ul>
@@ -63,7 +63,7 @@ <h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2
 $ <span class="kw">nano</span> draft.txt</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Which Editor?</h2>
+<h2 id="which-editor"><span class="glyphicon glyphicon-pushpin"></span>Which Editor?</h2>
 </div>
 <div class="panel-body">
 <p>When we say, “<code>nano</code> is a text editor,” we really do mean “text”: it can only work with plain character data, not tables, images, or any other human-friendly media. We use it in examples because almost anyone can drive it anywhere without training, but please use something more powerful for real work. On Unix systems (such as Linux and Mac OS X), many programmers use <a href="http://www.gnu.org/software/emacs/">Emacs</a> or <a href="http://www.vim.org/">Vim</a> (both of which are completely unintuitive, even by Unix standards), or a graphical editor such as <a href="http://projects.gnome.org/gedit/">Gedit</a>. On Windows, you may wish to use <a href="http://notepad-plus-plus.org/">Notepad++</a>.</p>
@@ -72,7 +72,8 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Which Editor?</h2>
 </aside>
 <p>Let’s type in a few lines of text, then use Control-O to write our data to disk:</p>
 <div class="figure">
-<img src="fig/nano-screenshot.png" alt="Nano in action" /><p class="caption">Nano in action</p>
+<img src="fig/nano-screenshot.png" alt="Nano in action" />
+<p class="caption">Nano in action</p>
 </div>
 <p>Once our file is saved, we can use Control-X to quit the editor and return to the shell. (Unix documentation often uses the shorthand <code>^A</code> to mean “control-A”.) <code>nano</code> doesn’t leave any output on the screen after it exits, but <code>ls</code> now shows that we have created a file called <code>draft.txt</code>:</p>
 <pre class="sourceCode bash"><code class="sourceCode bash">$ <span class="kw">ls</span></code></pre>
@@ -83,7 +84,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Which Editor?</h2>
 <pre class="sourceCode bash"><code class="sourceCode bash">$ <span class="kw">ls</span></code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Deleting Is Forever</h2>
+<h2 id="deleting-is-forever"><span class="glyphicon glyphicon-pushpin"></span>Deleting Is Forever</h2>
 </div>
 <div class="panel-body">
 <p>The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unhooked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.</p>
@@ -108,7 +109,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Deleting Is Forever</h2>
 <pre class="sourceCode bash"><code class="sourceCode bash">$ <span class="kw">rmdir</span> thesis</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>With Great Power Comes Great Responsibility</h2>
+<h2 id="with-great-power-comes-great-responsibility"><span class="glyphicon glyphicon-pushpin"></span>With Great Power Comes Great Responsibility</h2>
 </div>
 <div class="panel-body">
 <p>Removing the files in a directory just so that we can remove the directory quickly becomes tedious. Instead, we can use <code>rm</code> with the <code>-r</code> flag (which stands for “recursive”):</p>
@@ -148,7 +149,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>With Great Power Comes Grea
 <p>This time it tells us that it can’t find <code>quotes.txt</code> in the current directory, but it does find the copy in <code>thesis</code> that we didn’t delete.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Another Useful Abbreviation</h2>
+<h2 id="another-useful-abbreviation"><span class="glyphicon glyphicon-pushpin"></span>Another Useful Abbreviation</h2>
 </div>
 <div class="panel-body">
 <p>The shell interprets the character <code>~</code> (tilde) at the start of a path to mean “the current user’s home directory”. For example, if Nelle’s home directory is <code>/Users/nelle</code>, then <code>~/data</code> is equivalent to <code>/Users/nelle/data</code>. This only works if it is the first character in the path: <code>here/there/~/elsewhere</code> is <em>not</em> <code>/Users/nelle/elsewhere</code>.</p>
@@ -156,7 +157,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Another Useful Abbreviation
 </aside>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Renaming files</h2>
+<h2 id="renaming-files"><span class="glyphicon glyphicon-pencil"></span>Renaming files</h2>
 </div>
 <div class="panel-body">
 <p>Suppose that you created a <code>.txt</code> file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it: <code>statstics.txt</code></p>
@@ -171,7 +172,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Renaming files</h2>
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Moving and Copying</h2>
+<h2 id="moving-and-copying"><span class="glyphicon glyphicon-pencil"></span>Moving and Copying</h2>
 </div>
 <div class="panel-body">
 <p>What is the output of the closing <code>ls</code> command in the sequence shown below?</p>
@@ -193,7 +194,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Moving and Copying</h2>
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Listing Directories and Files</h2>
+<h2 id="listing-directories-and-files"><span class="glyphicon glyphicon-pencil"></span>Listing Directories and Files</h2>
 </div>
 <div class="panel-body">
 <p>Suppose that:</p>
@@ -208,7 +209,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Listing Directories and File
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Copy with Multiple Filenames</h2>
+<h2 id="copy-with-multiple-filenames"><span class="glyphicon glyphicon-pencil"></span>Copy with Multiple Filenames</h2>
 </div>
 <div class="panel-body">
 <p>What does <code>cp</code> do when given several filenames and a directory name, as in:</p>
@@ -222,7 +223,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Copy with Multiple Filenames
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Listing Recursively and By Time</h2>
+<h2 id="listing-recursively-and-by-time"><span class="glyphicon glyphicon-pencil"></span>Listing Recursively and By Time</h2>
 </div>
 <div class="panel-body">
 <p>The command <code>ls -R</code> lists the contents of directories recursively, i.e., lists their sub-directories, sub-sub-directories, and so on in alphabetical order at each level. The command <code>ls -t</code> lists things by time of last change, with most recently changed files or directories first. In what order does <code>ls -R -t</code> display things?</p>
diff --git a/03-pipefilter.html b/03-pipefilter.html
index dca7a951d..5d2b9a866 100644
--- a/03-pipefilter.html
+++ b/03-pipefilter.html
@@ -30,7 +30,7 @@ <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Pipes and Filters</h2>
 <section class="objectives panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
+<h2 id="learning-objectives"><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
 </div>
 <div class="panel-body">
 <ul>
@@ -58,7 +58,7 @@ <h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2
  107  819 6081 total</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Wildcards</h2>
+<h2 id="wildcards"><span class="glyphicon glyphicon-pushpin"></span>Wildcards</h2>
 </div>
 <div class="panel-body">
 <p><code>*</code> is a <strong>wildcard</strong>. It matches zero or more characters, so <code>*.pdb</code> matches <code>ethane.pdb</code>, <code>propane.pdb</code>, and so on. On the other hand, <code>p*.pdb</code> only matches <code>pentane.pdb</code> and <code>propane.pdb</code>, because the ‘p’ at the front only matches itself.</p>
@@ -117,19 +117,20 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Wildcards</h2>
 <p>Here’s what happens when we run <code>wc -l *.pdb &gt; lengths.txt</code>. The shell starts by telling the computer to create a new process to run the <code>wc</code> program. Since we’ve provided some filenames as parameters, <code>wc</code> reads from them instead of from standard input. And since we’ve used <code>&gt;</code> to redirect output to a file, the shell connects the process’s standard output to that file.</p>
 <p>If we run <code>wc -l *.pdb | sort -n</code> instead, the shell creates two processes (one for each process in the pipe) so that <code>wc</code> and <code>sort</code> run simultaneously. The standard output of <code>wc</code> is fed directly to the standard input of <code>sort</code>; since there’s no redirection with <code>&gt;</code>, <code>sort</code>’s output goes to the screen. And if we run <code>wc -l *.pdb | sort -n | head -1</code>, we get three processes with data flowing from the files, through <code>wc</code> to <code>sort</code>, and from <code>sort</code> through <code>head</code> to the screen.</p>
 <div class="figure">
-<img src="fig/redirects-and-pipes.png" alt="Redirects and Pipes" /><p class="caption">Redirects and Pipes</p>
+<img src="fig/redirects-and-pipes.png" alt="Redirects and Pipes" />
+<p class="caption">Redirects and Pipes</p>
 </div>
 <p>This simple idea is why Unix has been so successful. Instead of creating enormous programs that try to do many different things, Unix programmers focus on creating lots of simple tools that each do one job well, and that work well with each other. This programming model is called “pipes and filters”. We’ve already seen pipes; a <strong>filter</strong> is a program like <code>wc</code> or <code>sort</code> that transforms a stream of input into a stream of output. Almost all of the standard Unix tools can work this way: unless told to do otherwise, they read from standard input, do something with what they’ve read, and write to standard output.</p>
 <p>The key is that any program that reads lines of text from standard input and writes lines of text to standard output can be combined with every other program that behaves this way as well. You can <em>and should</em> write your programs this way so that you and other people can put those programs into pipes to multiply their power.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Redirecting Input</h2>
+<h2 id="redirecting-input"><span class="glyphicon glyphicon-pushpin"></span>Redirecting Input</h2>
 </div>
 <div class="panel-body">
 <p>As well as using <code>&gt;</code> to redirect a program’s output, we can use <code>&lt;</code> to redirect its input, i.e., to read from a file instead of from standard input. For example, instead of writing <code>wc ammonia.pdb</code>, we could write <code>wc &lt; ammonia.pdb</code>. In the first case, <code>wc</code> gets a command line parameter telling it what file to open. In the second, <code>wc</code> doesn’t have any command line parameters, so it reads from standard input, but we have told the shell to send the contents of <code>ammonia.pdb</code> to <code>wc</code>’s standard input.</p>
 </div>
 </aside>
-<h3 id="nelles-pipeline-checking-files">Nelle’s Pipeline: Checking Files</h3>
+<h2 id="nelles-pipeline-checking-files">Nelle’s Pipeline: Checking Files</h2>
 <p>Nelle has run her samples through the assay machines and created 1520 files in the <code>north-pacific-gyre/2012-07-03</code> directory described earlier. As a quick sanity check, starting from her home directory, Nelle types:</p>
 <pre class="sourceCode bash"><code class="sourceCode bash">$ <span class="kw">cd</span> north-pacific-gyre/2012-07-03
 $ <span class="kw">wc</span> -l *.txt</code></pre>
@@ -161,7 +162,7 @@ <h3 id="nelles-pipeline-checking-files">Nelle’s Pipeline: Checking Files</h3>
 <p>Sure enough, when she checks the log on her laptop, there’s no depth recorded for either of those samples. Since it’s too late to get the information any other way, she must exclude those two files from her analysis. She could just delete them using <code>rm</code>, but there are actually some analyses she might do later where depth doesn’t matter, so instead, she’ll just be careful later on to select files using the wildcard expression <code>*[AB].txt</code>. As always, the ‘*’ matches any number of characters; the expression <code>[AB]</code> matches either an ‘A’ or a ‘B’, so this matches all the valid data files she has.</p>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>What does <code>sort -n</code> do?</h2>
+<h2 id="what-does-sort--n-do"><span class="glyphicon glyphicon-pencil"></span>What does <code>sort -n</code> do?</h2>
 </div>
 <div class="panel-body">
 <p>If we run <code>sort</code> on this file:</p>
@@ -187,7 +188,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>What does <code>sort -n</cod
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>What does <code>&lt;</code> mean?</h2>
+<h2 id="what-does-mean"><span class="glyphicon glyphicon-pencil"></span>What does <code>&lt;</code> mean?</h2>
 </div>
 <div class="panel-body">
 <p>What is the difference between:</p>
@@ -198,7 +199,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>What does <code>&lt;</code>
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>What does <code>&gt;&gt;</code> mean?</h2>
+<h2 id="what-does-mean-1"><span class="glyphicon glyphicon-pencil"></span>What does <code>&gt;&gt;</code> mean?</h2>
 </div>
 <div class="panel-body">
 <p>What is the difference between:</p>
@@ -210,7 +211,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>What does <code>&gt;&gt;</co
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Piping commands together</h2>
+<h2 id="piping-commands-together"><span class="glyphicon glyphicon-pencil"></span>Piping commands together</h2>
 </div>
 <div class="panel-body">
 <p>In our current directory, we want to find the 3 files which have the least number of lines. Which command listed below would work?</p>
@@ -224,7 +225,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Piping commands together</h2
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Why does <code>uniq</code> only remove adjacent duplicates?</h2>
+<h2 id="why-does-uniq-only-remove-adjacent-duplicates"><span class="glyphicon glyphicon-pencil"></span>Why does <code>uniq</code> only remove adjacent duplicates?</h2>
 </div>
 <div class="panel-body">
 <p>The command <code>uniq</code> removes adjacent duplicated lines from its input. For example, if a file <code>salmon.txt</code> contains:</p>
@@ -244,7 +245,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Why does <code>uniq</code> o
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Pipe reading comprehension</h2>
+<h2 id="pipe-reading-comprehension"><span class="glyphicon glyphicon-pencil"></span>Pipe reading comprehension</h2>
 </div>
 <div class="panel-body">
 <p>A file called <code>animals.txt</code> contains the following data:</p>
@@ -262,7 +263,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Pipe reading comprehension</
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Pipe construction</h2>
+<h2 id="pipe-construction"><span class="glyphicon glyphicon-pencil"></span>Pipe construction</h2>
 </div>
 <div class="panel-body">
 <p>The command:</p>
diff --git a/04-loop.html b/04-loop.html
index 893bb5d02..71e564c53 100644
--- a/04-loop.html
+++ b/04-loop.html
@@ -30,7 +30,7 @@ <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Loops</h2>
 <section class="objectives panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
+<h2 id="learning-objectives"><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
 </div>
 <div class="panel-body">
 <ul>
@@ -66,7 +66,7 @@ <h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2
 <p>Finally, the command that’s actually being run is our old friend <code>head</code>, so this loop prints out the first three lines of each data file in turn.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Follow the Prompt</h2>
+<h2 id="follow-the-prompt"><span class="glyphicon glyphicon-pushpin"></span>Follow the Prompt</h2>
 </div>
 <div class="panel-body">
 <p>The shell prompt changes from <code>$</code> to <code>&gt;</code> and back again as we were typing in our loop. The second prompt, <code>&gt;</code>, is different to remind us that we haven’t finished typing a complete command yet.</p>
@@ -102,7 +102,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Follow the Prompt</h2>
 <p>because then the first time through the loop, when <code>$filename</code> expanded to <code>basilisk.dat</code>, the shell would try to run <code>basilisk.dat</code> as a program. Finally, the <code>head</code> and <code>tail</code> combination selects lines 81-100 from whatever file is being processed.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Spaces in Names</h2>
+<h2 id="spaces-in-names"><span class="glyphicon glyphicon-pushpin"></span>Spaces in Names</h2>
 </div>
 <div class="panel-body">
 <p>Filename expansion in loops is another reason you should not use spaces in filenames. Suppose our data files are named:</p>
@@ -141,7 +141,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Spaces in Names</h2>
 <pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">mv</span> unicorn.dat original-unicorn.dat</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Measure Twice, Run Once</h2>
+<h2 id="measure-twice-run-once"><span class="glyphicon glyphicon-pushpin"></span>Measure Twice, Run Once</h2>
 </div>
 <div class="panel-body">
 <p>A loop is a way to do many things at once — or to make many mistakes at once if it does the wrong thing. One way to check what a loop <em>would</em> do is to echo the commands it would run instead of actually running them. For example, we could write our file renaming loop like this:</p>
@@ -188,7 +188,7 @@ <h2 id="nelles-pipeline-processing-files">Nelle’s Pipeline: Processing Files</
 <pre class="sourceCode bash"><code class="sourceCode bash">$ <span class="kw">for</span> <span class="kw">datafile</span> in *[AB].txt<span class="kw">;</span> <span class="kw">do</span> <span class="kw">echo</span> <span class="ot">$datafile</span><span class="kw">;</span> <span class="kw">bash</span> goostats <span class="ot">$datafile</span> stats-<span class="ot">$datafile</span><span class="kw">;</span> <span class="kw">done</span></code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Beginning and End</h2>
+<h2 id="beginning-and-end"><span class="glyphicon glyphicon-pushpin"></span>Beginning and End</h2>
 </div>
 <div class="panel-body">
 <p>We can move to the beginning of a line in the shell by typing <code>^A</code> (which means Control-A) and to the end using <code>^E</code>.</p>
@@ -202,7 +202,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Beginning and End</h2>
 <p>1518 times 5 seconds, divided by 60, tells her that her script will take about two hours to run. As a final check, she opens another terminal window, goes into <code>north-pacific-gyre/2012-07-03</code>, and uses <code>cat stats-NENE01729B.txt</code> to examine one of the output files. It looks good, so she decides to get some coffee and catch up on her reading.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Those Who Know History Can Choose to Repeat It</h2>
+<h2 id="those-who-know-history-can-choose-to-repeat-it"><span class="glyphicon glyphicon-pushpin"></span>Those Who Know History Can Choose to Repeat It</h2>
 </div>
 <div class="panel-body">
 <p>Another way to repeat previous work is to use the <code>history</code> command to get a list of the last few hundred commands that have been executed, and then to use <code>!123</code> (where “123” is replaced by the command number) to repeat one of those commands. For example, if Nelle types this:</p>
@@ -217,7 +217,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Those Who Know History Can
 </aside>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Variables in Loops</h2>
+<h2 id="variables-in-loops"><span class="glyphicon glyphicon-pencil"></span>Variables in Loops</h2>
 </div>
 <div class="panel-body">
 <p>Suppose that <code>ls</code> initially displays:</p>
@@ -237,7 +237,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Variables in Loops</h2>
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Saving to a File in a Loop - Part One</h2>
+<h2 id="saving-to-a-file-in-a-loop---part-one"><span class="glyphicon glyphicon-pencil"></span>Saving to a File in a Loop - Part One</h2>
 </div>
 <div class="panel-body">
 <p>In the same directory, what is the effect of this loop?</p>
@@ -256,7 +256,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Saving to a File in a Loop -
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Saving to a File in a Loop - Part Two</h2>
+<h2 id="saving-to-a-file-in-a-loop---part-two"><span class="glyphicon glyphicon-pencil"></span>Saving to a File in a Loop - Part Two</h2>
 </div>
 <div class="panel-body">
 <p>In another directory, where <code>ls</code> returns:</p>
@@ -276,7 +276,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Saving to a File in a Loop -
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Doing a Dry Run</h2>
+<h2 id="doing-a-dry-run"><span class="glyphicon glyphicon-pencil"></span>Doing a Dry Run</h2>
 </div>
 <div class="panel-body">
 <p>Suppose we want to preview the commands the following loop will execute without actually running those commands:</p>
@@ -299,7 +299,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Doing a Dry Run</h2>
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Nested Loops and Command-Line Expressions</h2>
+<h2 id="nested-loops-and-command-line-expressions"><span class="glyphicon glyphicon-pencil"></span>Nested Loops and Command-Line Expressions</h2>
 </div>
 <div class="panel-body">
 <p>The <code>expr</code> does simple arithmetic using command-line parameters:</p>
diff --git a/05-script.html b/05-script.html
index a93fa31d5..90adbc5f6 100644
--- a/05-script.html
+++ b/05-script.html
@@ -30,7 +30,7 @@ <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Shell Scripts</h2>
 <section class="objectives panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
+<h2 id="learning-objectives"><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
 </div>
 <div class="panel-body">
 <ul>
@@ -57,7 +57,7 @@ <h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2
 <p>Sure enough, our script’s output is exactly what we would get if we ran that pipeline directly.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Text vs. Whatever</h2>
+<h2 id="text-vs.whatever"><span class="glyphicon glyphicon-pushpin"></span>Text vs. Whatever</h2>
 </div>
 <div class="panel-body">
 <p>We usually call programs like Microsoft Word or LibreOffice Writer “text editors”, but we need to be a bit more careful when it comes to programming. By default, Microsoft Word uses <code>.docx</code> files to store not only text, but also formatting information about fonts, headings, and so on. This extra information isn’t stored as characters, and doesn’t mean anything to tools like <code>head</code>: they expect input files to contain nothing but the letters, digits, and punctuation on a standard computer keyboard. When editing programs, therefore, you must either use a plain text editor, or be careful to save files as plain text.</p>
@@ -82,7 +82,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Text vs. Whatever</h2>
 ATOM     13  H           1      -1.183   0.500  -1.412  1.00  0.00</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Double-Quotes Around Arguments</h2>
+<h2 id="double-quotes-around-arguments"><span class="glyphicon glyphicon-pushpin"></span>Double-Quotes Around Arguments</h2>
 </div>
 <div class="panel-body">
 <p>We put the <code>$1</code> inside of double-quotes in case the filename happens to contain any spaces. The shell uses whitespace to separate arguments, so we have to be careful when using arguments that might have whitespace in them. If we left out these quotes, and <code>$1</code> expanded to a filename like <code>methyl butane.pdb</code>, the command in the script would effectively be:</p>
@@ -121,7 +121,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Double-Quotes Around Argume
 163 ../creatures/unicorn.dat</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Why Isn’t It Doing Anything?</h2>
+<h2 id="why-isnt-it-doing-anything"><span class="glyphicon glyphicon-pushpin"></span>Why Isn’t It Doing Anything?</h2>
 </div>
 <div class="panel-body">
 <p>What happens if a script is supposed to process a bunch of files, but we don’t give it any filenames? For example, what if we type:</p>
@@ -147,7 +147,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Why Isn’t It Doing Anythi
 <p>After a moment’s work in an editor to remove the serial numbers on the commands, we have a completely accurate record of how we created that figure.</p>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Unnumbering</h2>
+<h2 id="unnumbering"><span class="glyphicon glyphicon-pushpin"></span>Unnumbering</h2>
 </div>
 <div class="panel-body">
 <p>Nelle could also use <code>colrm</code> (short for “column removal”) to remove the serial numbers on her previous commands. Its parameters are the range of characters to strip from its input:</p>
@@ -191,7 +191,7 @@ <h2 id="nelles-pipeline-creating-a-script">Nelle’s Pipeline: Creating a Script
 <p>The advantage is that this always selects the right files: she doesn’t have to remember to exclude the ‘Z’ files. The disadvantage is that it <em>always</em> selects just those files — she can’t run it on all files (including the ‘Z’ files), or on the ‘G’ or ‘H’ files her colleagues in Antarctica are producing, without editing the script. If she wanted to be more adventurous, she could modify her script to check for command-line parameters, and use <code>*[AB].txt</code> if none were provided. Of course, this introduces another tradeoff between flexibility and complexity.</p>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Variables in shell scripts</h2>
+<h2 id="variables-in-shell-scripts"><span class="glyphicon glyphicon-pencil"></span>Variables in shell scripts</h2>
 </div>
 <div class="panel-body">
 <p>In the molecules directory, you have a shell script called <code>script.sh</code> containing the following commands:</p>
@@ -210,7 +210,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Variables in shell scripts</
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>List unique species</h2>
+<h2 id="list-unique-species"><span class="glyphicon glyphicon-pencil"></span>List unique species</h2>
 </div>
 <div class="panel-body">
 <p>Leah has several hundred data files, each of which is formatted like this:</p>
@@ -227,7 +227,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>List unique species</h2>
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Find the longest file with a given extension</h2>
+<h2 id="find-the-longest-file-with-a-given-extension"><span class="glyphicon glyphicon-pencil"></span>Find the longest file with a given extension</h2>
 </div>
 <div class="panel-body">
 <p>Write a shell script called <code>longest.sh</code> that takes the name of a directory and a filename extension as its parameters, and prints out the name of the file with the most lines in that directory with that extension. For example:</p>
@@ -237,7 +237,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Find the longest file with a
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Why record commands in the history before running them?</h2>
+<h2 id="why-record-commands-in-the-history-before-running-them"><span class="glyphicon glyphicon-pencil"></span>Why record commands in the history before running them?</h2>
 </div>
 <div class="panel-body">
 <p>If you run the command:</p>
@@ -247,7 +247,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Why record commands in the h
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Script reading comprehension</h2>
+<h2 id="script-reading-comprehension"><span class="glyphicon glyphicon-pencil"></span>Script reading comprehension</h2>
 </div>
 <div class="panel-body">
 <p>Joel’s <code>data</code> directory contains three files: <code>fructose.dat</code>, <code>glucose.dat</code>, and <code>sucrose.dat</code>. Explain what a script called <code>example.sh</code> would do when run as <code>bash example.sh *.dat</code> if it contained the following lines:</p>
diff --git a/06-find.html b/06-find.html
index 6b36b37d1..81a46b7d5 100644
--- a/06-find.html
+++ b/06-find.html
@@ -30,7 +30,7 @@ <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Finding Things</h2>
 <section class="objectives panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
+<h2 id="learning-objectives"><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2>
 </div>
 <div class="panel-body">
 <ul>
@@ -59,7 +59,7 @@ <h2><span class="glyphicon glyphicon-certificate"></span>Learning Objectives</h2
 Software is like that.</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Forever, or Five Years</h2>
+<h2 id="forever-or-five-years"><span class="glyphicon glyphicon-pushpin"></span>Forever, or Five Years</h2>
 </div>
 <div class="panel-body">
 <p>We haven’t linked to the original haikus because they don’t appear to be on <em>Salon</em>’s site any longer. As <a href="http://www.clir.org/pubs/archives/ensuring.pdf">Jeff Rothenberg said</a>, “Digital information lasts forever — or five years, whichever comes first.”</p>
@@ -142,7 +142,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Forever, or Five Years</h2>
 ...        ...        ...</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Wildcards</h2>
+<h2 id="wildcards"><span class="glyphicon glyphicon-pushpin"></span>Wildcards</h2>
 </div>
 <div class="panel-body">
 <p><code>grep</code>‘s real power doesn’t come from its options, though; it comes from the fact that patterns can include wildcards. (The technical name for these is <strong>regular expressions</strong>, which is what the “re” in “grep” stands for.) Regular expressions are both complex and powerful; if you want to do complex searches, please look at the lesson on <a href="http://software-carpentry.org/v4/regexp/index.html">our website</a>. As a taster, we can find lines that have an ’o’ in the second position like this:</p>
@@ -155,7 +155,8 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Wildcards</h2>
 </aside>
 <p>While <code>grep</code> finds lines in files, the <code>find</code> command finds files themselves. Again, it has a lot of options; to show how the simplest ones work, we’ll use the directory tree shown below.</p>
 <div class="figure">
-<img src="fig/find-file-tree.svg" alt="File Tree for Find Example" /><p class="caption">File Tree for Find Example</p>
+<img src="fig/find-file-tree.svg" alt="File Tree for Find Example" />
+<p class="caption">File Tree for Find Example</p>
 </div>
 <p>Nelle’s <code>writing</code> directory contains one file called <code>haiku.txt</code> and four subdirectories: <code>thesis</code> (which is sadly empty), <code>data</code> (which contains two files <code>one.txt</code> and <code>two.txt</code>), a <code>tools</code> directory that contains the programs <code>format</code> and <code>stats</code>, and an empty subdirectory called <code>old</code>.</p>
 <p>For our first command, let’s run <code>find . -type d</code>. As always, the <code>.</code> on its own means the current working directory, which is where we want our search to start; <code>-type d</code> means “things that are directories”. Sure enough, <code>find</code>’s output is the names of the five directories in our little tree (including <code>.</code>):</p>
@@ -196,7 +197,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Wildcards</h2>
 ./haiku.txt</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Listing vs. Finding</h2>
+<h2 id="listing-vs.finding"><span class="glyphicon glyphicon-pushpin"></span>Listing vs. Finding</h2>
 </div>
 <div class="panel-body">
 <p><code>ls</code> and <code>find</code> can be made to do similar things given the right options, but under normal circumstances, <code>ls</code> lists everything it can, while <code>find</code> searches for things with certain properties and shows them.</p>
@@ -217,7 +218,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Listing vs. Finding</h2>
 <pre class="output"><code>../data/pdb/heme.pdb:ATOM     25 FE           1      -0.924   0.535  -0.518</code></pre>
 <aside class="callout panel panel-info">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pushpin"></span>Binary Files</h2>
+<h2 id="binary-files"><span class="glyphicon glyphicon-pushpin"></span>Binary Files</h2>
 </div>
 <div class="panel-body">
 <p>We have focused exclusively on finding things in text files. What if your data is stored as images, in databases, or in some other format? One option would be to extend tools like <code>grep</code> to handle those formats. This hasn’t happened, and probably won’t, because there are too many formats to support.</p>
@@ -228,7 +229,7 @@ <h2><span class="glyphicon glyphicon-pushpin"></span>Binary Files</h2>
 <p>The Unix shell is older than most of the people who use it. It has survived so long because it is one of the most productive programming environments ever created — maybe even <em>the</em> most productive. Its syntax may be cryptic, but people who have mastered it can experiment with different commands interactively, then use what they have learned to automate their work. Graphical user interfaces may be better at the first, but the shell is still unbeaten at the second. And as Alfred North Whitehead wrote in 1911, “Civilization advances by extending the number of important operations which we can perform without thinking about them.”</p>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Using grep</h2>
+<h2 id="using-grep"><span class="glyphicon glyphicon-pencil"></span>Using grep</h2>
 </div>
 <div class="panel-body">
 <pre><code>The Tao that is seen
@@ -254,7 +255,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Using grep</h2>
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span><code>find</code> pipeline reading comprehension</h2>
+<h2 id="find-pipeline-reading-comprehension"><span class="glyphicon glyphicon-pencil"></span><code>find</code> pipeline reading comprehension</h2>
 </div>
 <div class="panel-body">
 <p>Write a short explanatory comment for the following shell script:</p>
@@ -263,7 +264,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span><code>find</code> pipeline r
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Matching <code>ose.dat</code> but not <code>temp</code></h2>
+<h2 id="matching-ose.dat-but-not-temp"><span class="glyphicon glyphicon-pencil"></span>Matching <code>ose.dat</code> but not <code>temp</code></h2>
 </div>
 <div class="panel-body">
 <p>The <code>-v</code> flag to <code>grep</code> inverts pattern matching, so that only lines which do <em>not</em> match the pattern are printed. Given that, which of the following commands will find all files in <code>/data</code> whose names end in <code>ose.dat</code> (e.g., <code>sucrose.dat</code> or <code>maltose.dat</code>), but do <em>not</em> contain the word <code>temp</code>?</p>
@@ -277,7 +278,7 @@ <h2><span class="glyphicon glyphicon-pencil"></span>Matching <code>ose.dat</code
 </section>
 <section class="challenge panel panel-success">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-pencil"></span>Little Women</h2>
+<h2 id="little-women"><span class="glyphicon glyphicon-pencil"></span>Little Women</h2>
 </div>
 <div class="panel-body">
 <p>You and your friend, having just finished reading <em>Little Women</em> by Louisa May Alcott, are in an argument. Of the four sisters in the book, Jo, Meg, Beth, and Amy, your friend thinks that Jo was the most mentioned. You, however, are certain it was Amy. Luckily, you have a file <code>LittleWomen.txt</code> containing the full text of the novel. Using a<code>for</code> loop, how would you tabulate the number of times each of the four sisters is mentioned? Hint: one solution might employ the commands <code>grep</code> and <code>wc</code> and a <code>|</code>, while another might utilize <code>grep</code> options.</p>
diff --git a/discussion.html b/discussion.html
index 97b1ee8ee..67831ffa0 100644
--- a/discussion.html
+++ b/discussion.html
@@ -28,7 +28,7 @@
         <div class="col-md-10 col-md-offset-1">
           <h1 class="title">The Unix Shell</h1>
           <h2 class="subtitle">Discussion</h2>
-<h3 id="other-shells">Other Shells</h3>
+<h2 id="other-shells">Other Shells</h2>
 <p>Before Bash became popular in the end of nineties, scientists widely used (and some still use) another shell, C-shell, or Csh. Bash and Csh have similar feature sets, but their syntax rules are different and this makes them incompatible with each other. A few other shells have appeared since, including ksh, zsh, and a number of others; they are mostly compatible with Bash, and Bash is the default shell on most modern implementations of Unix (including most packages that provide Unix-like tools for Windows) but if you get strange errors in shell scripts written by colleagues, check to see which shell they were written for.</p>
         </div>
       </div>
diff --git a/index.html b/index.html
index 4fa6d6db8..ada2d96eb 100644
--- a/index.html
+++ b/index.html
@@ -31,16 +31,16 @@ <h1 class="title">The Unix Shell</h1>
 <p>The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so that they don’t have to type the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively.</p>
 <section class="prereq panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-education"></span>Prerequisites</h2>
+<h2 id="prerequisites"><span class="glyphicon glyphicon-education"></span>Prerequisites</h2>
 </div>
 <div class="panel-body">
 <p>This lesson guides you through the basics of file systems and the shell. If you have stored files on a computer at all and recognize the word “file” and either “directory” or “folder” (two common words for the same thing), you’re ready for this lesson.</p>
 <p>If you’re already comfortable manipulating files and directories, searching for files with <code>grep</code> and <code>find</code>, and writing simple loops and scripts, you probably won’t learn much from this lesson.</p>
 </div>
 </section>
-<section class="prereq panel panel-warning">
+<section class="getready panel panel-warning">
 <div class="panel-heading">
-<h2><span class="glyphicon glyphicon-education"></span>Getting ready</h2>
+<h2 id="getting-ready"><span class="glyphicon glyphicon-check"></span>Getting ready</h2>
 </div>
 <div class="panel-body">
 <p>You need to download some files to follow this lesson:</p>
diff --git a/reference.html b/reference.html
index 25588e053..08f3e0dfa 100644
--- a/reference.html
+++ b/reference.html
@@ -111,7 +111,7 @@ <h2 id="glossary">Glossary</h2>
 <dd>A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with <a href="#parameter">parameter</a>.
 </dd>
 <dt><span id="command-shell">command shell</span></dt>
-<dd>FIXME
+<dd>See <a href="#shell">shell</a>
 </dd>
 <dt><span id="command-line-interface">command-line interface</span></dt>
 <dd>An interface based on typing commands, usually at a <a href="#read-evaluate-print-loop">REPL</a>. See also: <a href="#graphical-user-interface">graphical user interface</a>.