List children also when excluded from main navigation

- Limit the effect of `nav_exclude: true` to the main navigation.
- Include links to excluded pages in auto-generating lists of child pages
and in breadcrumbs.
- Refactor implementation by moving assignment of `first_level_url` and `second_level_url` from `_includes/nav.html` to `_layouts/default.html`.
- Clarify the effect of `nav_exclude` in the documentation.

_layouts/default.html

@@ -101,6 +101,21 @@ layout: table_wrappers
     <div id="main-content-wrap" class="main-content-wrap">
       {% unless page.url == "/" %}
         {% if page.parent %}
+          {%- for node in pages_list -%}
+            {%- if node.parent == nil -%}
+              {%- if page.parent == node.title or page.grand_parent == node.title -%}
+                {%- assign first_level_url = node.url | absolute_url -%}
+              {%- endif -%}
+              {%- if node.has_children -%}
+                {%- assign children_list = pages_list | where: "parent", node.title -%}
+                {%- for child in children_list -%}
+                  {%- if page.url == child.url or page.parent == child.title -%}
+                    {%- assign second_level_url = child.url | absolute_url -%}
+                  {%- endif -%}
+                {%- endfor -%}
+              {%- endif -%}
+            {%- endif -%}
+          {%- endfor -%}
           <nav aria-label="Breadcrumb" class="breadcrumb-nav">
             <ol class="breadcrumb-nav-list">
               {% if page.grand_parent %}