Reorganizing

36 files changed, 18 insertions, 588 deletions

diff --git a/_includes/head.html b/_includes/head.html
index 3b4228a..e80b4f9 100644
--- a/_includes/head.html
+++ b/_includes/head.html
@@ -11,11 +11,10 @@
 
   <script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
-  <!-- <link rel="stylesheet" href="{{ "/css/main.css" | prepend: site.baseurl }}"> -->
-  <link rel="stylesheet" href="{{ site.baseurl }}/tufte.css"/>
-  <link rel="stylesheet" href="{{ site.baseurl }}/latex.css"/>
-  <link rel="stylesheet" href="{{ site.baseurl }}/custom.css"/>
-  <link rel="stylesheet" href="{{ site.baseurl }}/github.css"/>
+  <link rel="stylesheet" href="{{ site.baseurl }}/resources/css/tufte.css"/>
+  <link rel="stylesheet" href="{{ site.baseurl }}/resources/css/latex.css"/>
+  <link rel="stylesheet" href="{{ site.baseurl }}/resources/css/custom.css"/>
+  <link rel="stylesheet" href="{{ site.baseurl }}/resources/css/github.css"/>
   <!-- <link rel="canonical" href="{{ page.url | replace:'index.html','' | prepend: site.baseurl | prepend: site.url }}"> -->
-  <!-- <link rel="alternate" type="application/rss+xml" title="{{ site.title }}" href="{{ "/feed.xml" | prepend: site.baseurl | prepend: site.url }}"> -->
+  <link rel="alternate" type="application/rss+xml" title="{{ site.title }}" href="{{ "/feed.xml" | prepend: site.baseurl | prepend: site.url }}">
 </head>
diff --git a/_sass/_base.scss b/_sass/_base.scss
deleted file mode 100644
index 0883c3c..0000000
--- a/_sass/_base.scss
+++ /dev/null
@@ -1,206 +0,0 @@
-/**
- * Reset some basic elements
- */
-body, h1, h2, h3, h4, h5, h6,
-p, blockquote, pre, hr,
-dl, dd, ol, ul, figure {
-    margin: 0;
-    padding: 0;
-}
-
-
-
-/**
- * Basic styling
- */
-body {
-    font: $base-font-weight #{$base-font-size}/#{$base-line-height} $base-font-family;
-    color: $text-color;
-    background-color: $background-color;
-    -webkit-text-size-adjust: 100%;
-    -webkit-font-feature-settings: "kern" 1;
-    -moz-font-feature-settings: "kern" 1;
-    -o-font-feature-settings: "kern" 1;
-    font-feature-settings: "kern" 1;
-    font-kerning: normal;
-}
-
-
-
-/**
- * Set `margin-bottom` to maintain vertical rhythm
- */
-h1, h2, h3, h4, h5, h6,
-p, blockquote, pre,
-ul, ol, dl, figure,
-%vertical-rhythm {
-    margin-bottom: $spacing-unit / 2;
-}
-
-
-
-/**
- * Images
- */
-img {
-    max-width: 100%;
-    vertical-align: middle;
-}
-
-
-
-/**
- * Figures
- */
-figure > img {
-    display: block;
-}
-
-figcaption {
-    font-size: $small-font-size;
-}
-
-
-
-/**
- * Lists
- */
-ul, ol {
-    margin-left: $spacing-unit;
-}
-
-li {
-    > ul,
-    > ol {
-         margin-bottom: 0;
-    }
-}
-
-
-
-/**
- * Headings
- */
-h1, h2, h3, h4, h5, h6 {
-    font-weight: $base-font-weight;
-}
-
-
-
-/**
- * Links
- */
-a {
-    color: $brand-color;
-    text-decoration: none;
-
-    &:visited {
-        color: darken($brand-color, 15%);
-    }
-
-    &:hover {
-        color: $text-color;
-        text-decoration: underline;
-    }
-}
-
-
-
-/**
- * Blockquotes
- */
-blockquote {
-    color: $grey-color;
-    border-left: 4px solid $grey-color-light;
-    padding-left: $spacing-unit / 2;
-    font-size: 18px;
-    letter-spacing: -1px;
-    font-style: italic;
-
-    > :last-child {
-        margin-bottom: 0;
-    }
-}
-
-
-
-/**
- * Code formatting
- */
-pre,
-code {
-    font-size: 15px;
-    border: 1px solid $grey-color-light;
-    border-radius: 3px;
-    background-color: #eef;
-}
-
-code {
-    padding: 1px 5px;
-}
-
-pre {
-    padding: 8px 12px;
-    overflow-x: auto;
-
-    > code {
-        border: 0;
-        padding-right: 0;
-        padding-left: 0;
-    }
-}
-
-
-
-/**
- * Wrapper
- */
-.wrapper {
-    max-width: -webkit-calc(#{$content-width} - (#{$spacing-unit} * 2));
-    max-width:         calc(#{$content-width} - (#{$spacing-unit} * 2));
-    margin-right: auto;
-    margin-left: auto;
-    padding-right: $spacing-unit;
-    padding-left: $spacing-unit;
-    @extend %clearfix;
-
-    @include media-query($on-laptop) {
-        max-width: -webkit-calc(#{$content-width} - (#{$spacing-unit}));
-        max-width:         calc(#{$content-width} - (#{$spacing-unit}));
-        padding-right: $spacing-unit / 2;
-        padding-left: $spacing-unit / 2;
-    }
-}
-
-
-
-/**
- * Clearfix
- */
-%clearfix {
-
-    &:after {
-        content: "";
-        display: table;
-        clear: both;
-    }
-}
-
-
-
-/**
- * Icons
- */
-.icon {
-
-    > svg {
-        display: inline-block;
-        width: 16px;
-        height: 16px;
-        vertical-align: middle;
-
-        path {
-            fill: $grey-color;
-        }
-    }
-}
diff --git a/_sass/_layout.scss b/_sass/_layout.scss
deleted file mode 100644
index 9cbfdde..0000000
--- a/_sass/_layout.scss
+++ /dev/null
@@ -1,242 +0,0 @@
-/**
- * Site header
- */
-.site-header {
-    border-top: 5px solid $grey-color-dark;
-    border-bottom: 1px solid $grey-color-light;
-    min-height: 56px;
-
-    // Positioning context for the mobile navigation icon
-    position: relative;
-}
-
-.site-title {
-    font-size: 26px;
-    font-weight: 300;
-    line-height: 56px;
-    letter-spacing: -1px;
-    margin-bottom: 0;
-    float: left;
-
-    &,
-    &:visited {
-        color: $grey-color-dark;
-    }
-}
-
-.site-nav {
-    float: right;
-    line-height: 56px;
-
-    .menu-icon {
-        display: none;
-    }
-
-    .page-link {
-        color: $text-color;
-        line-height: $base-line-height;
-
-        // Gaps between nav items, but not on the last one
-        &:not(:last-child) {
-            margin-right: 20px;
-        }
-    }
-
-    @include media-query($on-palm) {
-        position: absolute;
-        top: 9px;
-        right: $spacing-unit / 2;
-        background-color: $background-color;
-        border: 1px solid $grey-color-light;
-        border-radius: 5px;
-        text-align: right;
-
-        .menu-icon {
-            display: block;
-            float: right;
-            width: 36px;
-            height: 26px;
-            line-height: 0;
-            padding-top: 10px;
-            text-align: center;
-
-            > svg {
-                width: 18px;
-                height: 15px;
-
-                path {
-                    fill: $grey-color-dark;
-                }
-            }
-        }
-
-        .trigger {
-            clear: both;
-            display: none;
-        }
-
-        &:hover .trigger {
-            display: block;
-            padding-bottom: 5px;
-        }
-
-        .page-link {
-            display: block;
-            padding: 5px 10px;
-
-            &:not(:last-child) {
-                margin-right: 0;
-            }
-            margin-left: 20px;
-        }
-    }
-}
-
-
-
-/**
- * Site footer
- */
-.site-footer {
-    border-top: 1px solid $grey-color-light;
-    padding: $spacing-unit 0;
-}
-
-.footer-heading {
-    font-size: 18px;
-    margin-bottom: $spacing-unit / 2;
-}
-
-.contact-list,
-.social-media-list {
-    list-style: none;
-    margin-left: 0;
-}
-
-.footer-col-wrapper {
-    font-size: 15px;
-    color: $grey-color;
-    margin-left: -$spacing-unit / 2;
-    @extend %clearfix;
-}
-
-.footer-col {
-    float: left;
-    margin-bottom: $spacing-unit / 2;
-    padding-left: $spacing-unit / 2;
-}
-
-.footer-col-1 {
-    width: -webkit-calc(35% - (#{$spacing-unit} / 2));
-    width:         calc(35% - (#{$spacing-unit} / 2));
-}
-
-.footer-col-2 {
-    width: -webkit-calc(20% - (#{$spacing-unit} / 2));
-    width:         calc(20% - (#{$spacing-unit} / 2));
-}
-
-.footer-col-3 {
-    width: -webkit-calc(45% - (#{$spacing-unit} / 2));
-    width:         calc(45% - (#{$spacing-unit} / 2));
-}
-
-@include media-query($on-laptop) {
-    .footer-col-1,
-    .footer-col-2 {
-        width: -webkit-calc(50% - (#{$spacing-unit} / 2));
-        width:         calc(50% - (#{$spacing-unit} / 2));
-    }
-
-    .footer-col-3 {
-        width: -webkit-calc(100% - (#{$spacing-unit} / 2));
-        width:         calc(100% - (#{$spacing-unit} / 2));
-    }
-}
-
-@include media-query($on-palm) {
-    .footer-col {
-        float: none;
-        width: -webkit-calc(100% - (#{$spacing-unit} / 2));
-        width:         calc(100% - (#{$spacing-unit} / 2));
-    }
-}
-
-
-
-/**
- * Page content
- */
-.page-content {
-    padding: $spacing-unit 0;
-}
-
-.page-heading {
-    font-size: 20px;
-}
-
-.post-list {
-    margin-left: 0;
-    list-style: none;
-
-    > li {
-        margin-bottom: $spacing-unit;
-    }
-}
-
-.post-meta {
-    font-size: $small-font-size;
-    color: $grey-color;
-}
-
-.post-link {
-    display: block;
-    font-size: 24px;
-}
-
-
-
-/**
- * Posts
- */
-.post-header {
-    margin-bottom: $spacing-unit;
-}
-
-.post-title {
-    font-size: 42px;
-    letter-spacing: -1px;
-    line-height: 1;
-
-    @include media-query($on-laptop) {
-        font-size: 36px;
-    }
-}
-
-.post-content {
-    margin-bottom: $spacing-unit;
-
-    h2 {
-        font-size: 32px;
-
-        @include media-query($on-laptop) {
-            font-size: 28px;
-        }
-    }
-
-    h3 {
-        font-size: 26px;
-
-        @include media-query($on-laptop) {
-            font-size: 22px;
-        }
-    }
-
-    h4 {
-        font-size: 20px;
-
-        @include media-query($on-laptop) {
-            font-size: 18px;
-        }
-    }
-}
diff --git a/_sass/_syntax-highlighting.scss b/_sass/_syntax-highlighting.scss
deleted file mode 100644
index 8fac597..0000000
--- a/_sass/_syntax-highlighting.scss
+++ /dev/null
@@ -1,71 +0,0 @@
-/**
- * Syntax highlighting styles
- */
-.highlight {
-    background: #fff;
-    @extend %vertical-rhythm;
-
-    .highlighter-rouge & {
-      background: #eef;
-    }
-
-    .c     { color: #998; font-style: italic } // Comment
-    .err   { color: #a61717; background-color: #e3d2d2 } // Error
-    .k     { font-weight: bold } // Keyword
-    .o     { font-weight: bold } // Operator
-    .cm    { color: #998; font-style: italic } // Comment.Multiline
-    .cp    { color: #999; font-weight: bold } // Comment.Preproc
-    .c1    { color: #998; font-style: italic } // Comment.Single
-    .cs    { color: #999; font-weight: bold; font-style: italic } // Comment.Special
-    .gd    { color: #000; background-color: #fdd } // Generic.Deleted
-    .gd .x { color: #000; background-color: #faa } // Generic.Deleted.Specific
-    .ge    { font-style: italic } // Generic.Emph
-    .gr    { color: #a00 } // Generic.Error
-    .gh    { color: #999 } // Generic.Heading
-    .gi    { color: #000; background-color: #dfd } // Generic.Inserted
-    .gi .x { color: #000; background-color: #afa } // Generic.Inserted.Specific
-    .go    { color: #888 } // Generic.Output
-    .gp    { color: #555 } // Generic.Prompt
-    .gs    { font-weight: bold } // Generic.Strong
-    .gu    { color: #aaa } // Generic.Subheading
-    .gt    { color: #a00 } // Generic.Traceback
-    .kc    { font-weight: bold } // Keyword.Constant
-    .kd    { font-weight: bold } // Keyword.Declaration
-    .kp    { font-weight: bold } // Keyword.Pseudo
-    .kr    { font-weight: bold } // Keyword.Reserved
-    .kt    { color: #458; font-weight: bold } // Keyword.Type
-    .m     { color: #099 } // Literal.Number
-    .s     { color: #d14 } // Literal.String
-    .na    { color: #008080 } // Name.Attribute
-    .nb    { color: #0086B3 } // Name.Builtin
-    .nc    { color: #458; font-weight: bold } // Name.Class
-    .no    { color: #008080 } // Name.Constant
-    .ni    { color: #800080 } // Name.Entity
-    .ne    { color: #900; font-weight: bold } // Name.Exception
-    .nf    { color: #900; font-weight: bold } // Name.Function
-    .nn    { color: #555 } // Name.Namespace
-    .nt    { color: #000080 } // Name.Tag
-    .nv    { color: #008080 } // Name.Variable
-    .ow    { font-weight: bold } // Operator.Word
-    .w     { color: #bbb } // Text.Whitespace
-    .mf    { color: #099 } // Literal.Number.Float
-    .mh    { color: #099 } // Literal.Number.Hex
-    .mi    { color: #099 } // Literal.Number.Integer
-    .mo    { color: #099 } // Literal.Number.Oct
-    .sb    { color: #d14 } // Literal.String.Backtick
-    .sc    { color: #d14 } // Literal.String.Char
-    .sd    { color: #d14 } // Literal.String.Doc
-    .s2    { color: #d14 } // Literal.String.Double
-    .se    { color: #d14 } // Literal.String.Escape
-    .sh    { color: #d14 } // Literal.String.Heredoc
-    .si    { color: #d14 } // Literal.String.Interpol
-    .sx    { color: #d14 } // Literal.String.Other
-    .sr    { color: #009926 } // Literal.String.Regex
-    .s1    { color: #d14 } // Literal.String.Single
-    .ss    { color: #990073 } // Literal.String.Symbol
-    .bp    { color: #999 } // Name.Builtin.Pseudo
-    .vc    { color: #008080 } // Name.Variable.Class
-    .vg    { color: #008080 } // Name.Variable.Global
-    .vi    { color: #008080 } // Name.Variable.Instance
-    .il    { color: #099 } // Literal.Number.Integer.Long
-}
diff --git a/css/main.scss b/css/main.scss
deleted file mode 100644
index f2e566e..0000000
--- a/css/main.scss
+++ /dev/null
@@ -1,53 +0,0 @@
----
-# Only the main Sass file needs front matter (the dashes are enough)
----
-@charset "utf-8";
-
-
-
-// Our variables
-$base-font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
-$base-font-size:   16px;
-$base-font-weight: 400;
-$small-font-size:  $base-font-size * 0.875;
-$base-line-height: 1.5;
-
-$spacing-unit:     30px;
-
-$text-color:       #111;
-$background-color: #fdfdfd;
-$brand-color:      #2a7ae2;
-
-$grey-color:       #828282;
-$grey-color-light: lighten($grey-color, 40%);
-$grey-color-dark:  darken($grey-color, 25%);
-
-// Width of the content area
-$content-width:    800px;
-
-$on-palm:          600px;
-$on-laptop:        800px;
-
-
-
-// Use media queries like this:
-// @include media-query($on-palm) {
-//     .wrapper {
-//         padding-right: $spacing-unit / 2;
-//         padding-left: $spacing-unit / 2;
-//     }
-// }
-@mixin media-query($device) {
-    @media screen and (max-width: $device) {
-        @content;
-    }
-}
-
-
-
-// Import partials from `sass_dir` (defaults to `_sass`)
-@import
-        "base",
-        "layout",
-        "syntax-highlighting"
-;
diff --git a/example.md b/example.md
index 9e1086b..b4367a5 100644
--- a/example.md
+++ b/example.md
@@ -17,7 +17,7 @@ print_hi('Tom')
 #=> prints 'Hi, Tom' to STDOUT.
 ```
 
-Check out the [Jekyll docs][jekyll-docs] for more info on how to get the most out of Jekyll. File all bugs/feature requests at [Jekyll’s GitHub repo][jekyll-gh]. If you have questions, you can ask them on [Jekyll Talk][jekyll-talk].
+Check out the [Jekyll docs](https://jekyllrb.com/docs/home/) for more info on how to get the most out of Jekyll. File all bugs/feature requests at [Jekyll’s GitHub repo](https://github.com/jekyll/jekyll). If you have questions, you can ask them on [Jekyll Talk](https://talk.jekyllrb.com/).
 
 ## Header
 
@@ -46,7 +46,7 @@ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor i
 Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. {% cite Uniqueness %}
 
 <figure class="fullwidth">
-  <img src="{{ site.baseurl }}/img/napoleons-march.png" alt="Figurative map of the successive losses of the French Army in the Russian campaign, 1812-1813" />
+  <img src="{{ site.baseurl }}/resources/img/napoleons-march.png" alt="Figurative map of the successive losses of the French Army in the Russian campaign, 1812-1813" />
 </figure>
 
 Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. {% cite Elsman2005 Kennedy2004 %}
diff --git a/custom.css b/resources/css/custom.css
index 75960e0..75960e0 100644
--- a/custom.css
+++ b/resources/css/custom.css
diff --git a/github.css b/resources/css/github.css
index 4cf358a..4cf358a 100644
--- a/github.css
+++ b/resources/css/github.css
diff --git a/latex.css b/resources/css/latex.css
index 2db66ef..2db66ef 100755
--- a/latex.css
+++ b/resources/css/latex.css
diff --git a/tufte.css b/resources/css/tufte.css
index 3d9275d..fddf62a 100755
--- a/tufte.css
+++ b/resources/css/tufte.css
@@ -1,29 +1,32 @@
+---
+---
+
 /* Import ET Book styles
    adapted from https://github.com/edwardtufte/et-book/blob/gh-pages/et-book.css */
 
 @charset "UTF-8";
 
 @font-face { font-family: "et-book";
-             src: url("et-book/et-book-roman-line-figures/et-book-roman-line-figures.eot");
-             src: url("et-book/et-book-roman-line-figures/et-book-roman-line-figures.eot?#iefix") format("embedded-opentype"), url("et-book/et-book-roman-line-figures/et-book-roman-line-figures.woff") format("woff"), url("et-book/et-book-roman-line-figures/et-book-roman-line-figures.ttf") format("truetype"), url("et-book/et-book-roman-line-figures/et-book-roman-line-figures.svg#etbookromanosf") format("svg");
+             src: url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-roman-line-figures/et-book-roman-line-figures.eot");
+             src: url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-roman-line-figures/et-book-roman-line-figures.eot?#iefix") format("embedded-opentype"), url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-roman-line-figures/et-book-roman-line-figures.woff") format("woff"), url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-roman-line-figures/et-book-roman-line-figures.ttf") format("truetype"), url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-roman-line-figures/et-book-roman-line-figures.svg#etbookromanosf") format("svg");
              font-weight: normal;
              font-style: normal; }
 
 @font-face { font-family: "et-book";
-             src: url("et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.eot");
-             src: url("et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.eot?#iefix") format("embedded-opentype"), url("et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.woff") format("woff"), url("et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.ttf") format("truetype"), url("et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.svg#etbookromanosf") format("svg");
+             src: url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.eot");
+             src: url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.eot?#iefix") format("embedded-opentype"), url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.woff") format("woff"), url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.ttf") format("truetype"), url("{{ site.baseurl }}/resources/glyphs/et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.svg#etbookromanosf") format("svg");
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