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Try including anchor headings via allejo/jekyll-anchor-headings.
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_includes/anchor_headings.html

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{% capture headingsWorkspace %}
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{% comment %}
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Copyright (c) 2018 Vladimir "allejo" Jimenez
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Permission is hereby granted, free of charge, to any person
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obtaining a copy of this software and associated documentation
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files (the "Software"), to deal in the Software without
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restriction, including without limitation the rights to use,
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copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following
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conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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OTHER DEALINGS IN THE SOFTWARE.
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{% endcomment %}
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{% comment %}
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Version 1.0.11
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https://github.com/allejo/jekyll-anchor-headings
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"Be the pull request you wish to see in the world." ~Ben Balter
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Usage:
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{% include anchor_headings.html html=content anchorBody="#" %}
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Parameters:
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* html (string) - the HTML of compiled markdown generated by kramdown in Jekyll
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Optional Parameters:
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* beforeHeading (bool) : false - Set to true if the anchor should be placed _before_ the heading's content
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* headerAttrs (string) : '' - Any custom HTML attributes that will be added to the heading tag; you may NOT use `id`;
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the `%heading%` and `%html_id%` placeholders are available
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* anchorAttrs (string) : '' - Any custom HTML attributes that will be added to the `<a>` tag; you may NOT use `href`, `class` or `title`;
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the `%heading%` and `%html_id%` placeholders are available
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* anchorBody (string) : '' - The content that will be placed inside the anchor; the `%heading%` placeholder is available
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* anchorClass (string) : '' - The class(es) that will be used for each anchor. Separate multiple classes with a space
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* anchorTitle (string) : '' - The `title` attribute that will be used for anchors
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* h_min (int) : 1 - The minimum header level to build an anchor for; any header lower than this value will be ignored
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* h_max (int) : 6 - The maximum header level to build an anchor for; any header greater than this value will be ignored
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* bodyPrefix (string) : '' - Anything that should be inserted inside of the heading tag _before_ its anchor and content
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* bodySuffix (string) : '' - Anything that should be inserted inside of the heading tag _after_ its anchor and content
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* generateId (true) : false - Set to true if a header without id should generate an id to use.
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Output:
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The original HTML with the addition of anchors inside of all of the h1-h6 headings.
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{% endcomment %}
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{% assign minHeader = include.h_min | default: 1 %}
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{% assign maxHeader = include.h_max | default: 6 %}
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{% assign beforeHeading = include.beforeHeading %}
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{% assign headerAttrs = include.headerAttrs %}
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{% assign nodes = include.html | split: '<h' %}
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{% capture edited_headings %}{% endcapture %}
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{% for _node in nodes %}
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{% capture node %}{{ _node | strip }}{% endcapture %}
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{% if node == "" %}
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{% continue %}
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{% endif %}
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{% assign nextChar = node | replace: '"', '' | strip | slice: 0, 1 %}
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{% assign headerLevel = nextChar | times: 1 %}
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<!-- If the level is cast to 0, it means it's not a h1-h6 tag, so let's see if we need to fix it -->
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{% if headerLevel == 0 %}
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<!-- Split up the node based on closing angle brackets and get the first one. -->
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{% assign firstChunk = node | split: '>' | first %}
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<!-- If the first chunk does NOT contain a '<', that means we've broken another HTML tag that starts with 'h' -->
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{% unless firstChunk contains '<' %}
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{% capture node %}<h{{ node }}{% endcapture %}
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{% endunless %}
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{% capture edited_headings %}{{ edited_headings }}{{ node }}{% endcapture %}
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{% continue %}
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{% endif %}
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{% capture _closingTag %}</h{{ headerLevel }}>{% endcapture %}
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{% assign _workspace = node | split: _closingTag %}
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{% capture _hAttrToStrip %}{{ _workspace[0] | split: '>' | first }}>{% endcapture %}
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{% assign header = _workspace[0] | replace: _hAttrToStrip, '' %}
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{% assign escaped_header = header | strip_html | strip %}
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{% assign _classWorkspace = _workspace[0] | split: 'class="' %}
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{% assign _classWorkspace = _classWorkspace[1] | split: '"' %}
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{% assign _html_class = _classWorkspace[0] %}
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{% if _html_class contains "no_anchor" %}
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{% assign skip_anchor = true %}
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{% else %}
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{% assign skip_anchor = false %}
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{% endif %}
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{% assign _idWorkspace = _workspace[0] | split: 'id="' %}
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{% if _idWorkspace[1] %}
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{% assign _idWorkspace = _idWorkspace[1] | split: '"' %}
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{% assign html_id = _idWorkspace[0] %}
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{% elsif include.generateId %}
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<!-- If the header did not have an id we create one. -->
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{% assign html_id = escaped_header | slugify %}
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{% if html_id == "" %}
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{% assign html_id = false %}
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{% endif %}
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{% capture headerAttrs %}{{ headerAttrs }} id="%html_id%"{% endcapture %}
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{% endif %}
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<!-- Build the anchor to inject for our heading -->
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{% capture anchor %}{% endcapture %}
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{% if skip_anchor == false and html_id and headerLevel >= minHeader and headerLevel <= maxHeader %}
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{% if headerAttrs %}
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{% capture _hAttrToStrip %}{{ _hAttrToStrip | split: '>' | first }} {{ headerAttrs | replace: '%heading%', escaped_header | replace: '%html_id%', html_id }}>{% endcapture %}
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{% endif %}
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{% capture anchor %}href="#{{ html_id }}"{% endcapture %}
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{% if include.anchorClass %}
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{% capture anchor %}{{ anchor }} class="{{ include.anchorClass }}"{% endcapture %}
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{% endif %}
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{% if include.anchorTitle %}
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{% capture anchor %}{{ anchor }} title="{{ include.anchorTitle | replace: '%heading%', escaped_header }}"{% endcapture %}
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{% endif %}
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{% if include.anchorAttrs %}
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{% capture anchor %}{{ anchor }} {{ include.anchorAttrs | replace: '%heading%', escaped_header | replace: '%html_id%', html_id }}{% endcapture %}
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{% endif %}
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{% capture anchor %}<a {{ anchor }}>{{ include.anchorBody | replace: '%heading%', escaped_header | default: '' }}</a>{% endcapture %}
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<!-- In order to prevent adding extra space after a heading, we'll let the 'anchor' value contain it -->
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{% if beforeHeading %}
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{% capture anchor %}{{ anchor }} {% endcapture %}
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{% else %}
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{% capture anchor %} {{ anchor }}{% endcapture %}
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{% endif %}
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{% endif %}
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{% capture new_heading %}
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<h{{ _hAttrToStrip }}
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{{ include.bodyPrefix }}
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{% if beforeHeading %}
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{{ anchor }}{{ header }}
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{% else %}
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{{ header }}{{ anchor }}
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{% endif %}
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{{ include.bodySuffix }}
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</h{{ headerLevel }}>
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{% endcapture %}
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<!--
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If we have content after the `</hX>` tag, then we'll want to append that here so we don't lost any content.
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-->
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{% assign chunkCount = _workspace | size %}
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{% if chunkCount > 1 %}
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{% capture new_heading %}{{ new_heading }}{{ _workspace | last }}{% endcapture %}
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{% endif %}
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{% capture edited_headings %}{{ edited_headings }}{{ new_heading }}{% endcapture %}
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{% endfor %}
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{% endcapture %}{% assign headingsWorkspace = '' %}{{ edited_headings | strip }}

_layouts/default.html

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<script async type="text/javascript" src="//cdn.carbonads.com/carbon.js?serve=CE7I627Y&placement=json-schemaorg" id="_carbonads_js"></script>
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{% endif %}
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<div class="wrapper">
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{{ content }}
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{% include anchor_headings.html html=content anchorBody="#" %}
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</div>
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</main>
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