A fix to display both link-list and tag generated navigation in the sidebar of the Clearflex theme. Many thanks to Caro (https://github.com/carolineschnapp) for her outstanding help and direction!

gistfile1.html

<!-- in collection-nav.liquid, replace this for loop code -->

{% for link in linklists.[settings.linklist_collections].links %}
<li class="collection{% if settings.show_collection_tags and link.object.all_tags.size > 0 %} dropdown{% endif %}">
  <a href="{{ link.url }}"{% if link.active %} class="current"{% endif %}>{{ link.title | escape }}</a>
  {% capture child_list_handle %}{{ link.title | handleize }}{% endcapture %}
  {% if linklists[child_list_handle] and linklists[child_list_handle].links.size > 0 %}
  <ul class="collection-tags">
    {% for l in linklists[child_list_handle].links %}
    <li><a href="{{ l.url }}">{{ l.title | escape }}</a></li>
    {% endfor %}
  </ul>
  {% elsif settings.show_collection_tags and link.object.all_tags.size > 0 %}
  <ul class="collection-tags">
    {% for tag in link.object.all_tags %}
    <li><a href="{{ link.url }}/{{ tag | handle }}">{{ tag | escape }}</a></li>
    {% endfor %}
  </ul>
  {% endif %}
</li>
{% endfor %}

<!-- in collection-list.liquid, replace this for loop code -->

{% for link in linklists[settings.linklist_collections].links %}
<li class="collection{% if link.active %} current{% endif %}">
  <a href="{{ link.url }}">{{ link.title }}</a>
  {% assign link_is_active = false %}
  {% assign has_drop_down = false %}
  {% assign list = '' %}
  {% capture child_link_list %}{{ link.title | handle }}{% endcapture %}
  {% if linklists[child_link_list].links.size > 0 %}
    {% assign has_drop_down = true %}          
    {% for l in linklists[child_link_list].links %}
    {% capture temp %}{{ list }} {{ l.title }} {% endcapture %}
    {% assign list = temp %}
    {% endfor %}
    {% if list contains page_title %}
      {% assign link_is_active = true %}
    {% endif %}
  {% endif %}
  {% if link.active or link_is_active %}
  {% if has_drop_down %}
  <ul class="collection-tags">
    {% for l in linklists[child_link_list].links %}
    <li{% if l.active %} class="current"{% endif %}><a href="{{ l.url }}">{{ l.title }}</a></li>
    {% endfor %}
  </ul>
  {% elsif settings.show_collection_tags and link.object.all_tags.size > 0 %}
  <ul class="collection-tags">
    {% for tag in link.object.all_tags %}
    <li{% if current_tags contains tag %} class="current"{% endif %}><a href="{{ link.url }}/{{ tag | handle }}">{{ tag }}</a></li>
    {% endfor %}
  </ul>
  {% endif %}
  {% endif %}
</li>
{% endfor %}