Magento 2 – How to Remove Categories from Layered Navigation

Yes, very possible, and I do exactly the same for a client site.

First I created a new attribute for categories, to allow me to set that a category needs to use the normal link. This is done via a module.

The module structure:

app/code/local/ProxiBlue/AttributeUseNormalFilterLink/
app/code/local/ProxiBlue/AttributeUseNormalFilterLink/Model/Mysql4/
app/code/local/ProxiBlue/AttributeUseNormalFilterLink/etc
app/code/local/ProxiBlue/AttributeUseNormalFilterLink/sql/proxiblue_filterlink_setup

In Model/Mysql4 I have file Setup.php Contents:

class ProxiBlue_AttributeUseNormalFilterLink_Model_Mysql4_Setup extends Mage_Catalog_Model_Resource_Setup {

    private $_category_attributes = array(
        'use_normal_filter_link' => array(
            'label' => 'Use normal filter link in left navigation',
            'type' => 'int',
            'input' => 'select',
            'source' => 'eav/entity_attribute_source_boolean',
            'default' => '0',
            'global' => Mage_Catalog_Model_Resource_Eav_Attribute::SCOPE_STORE,
            'visible' => true,
            'required' => false,
            'user_defined' => false,
            'visible_on_front' => true,
            'is_visible_on_front' =>true,
            'used_in_product_listing' => true,
        )
    );

    public function getDefaultEntities() {
        $entities = array();

        $default_attribute_options = array(
            'group' => 'General Information',
            'required' => false,
        );

        /* Build Catalog Attributes */
        $entities['catalog_category'] = array(
            'entity_model' => 'catalog/category',
            'attribute_model' => 'catalog/resource_eav_attribute',
            'table' => 'catalog/category',
            'additional_attribute_table' => 'catalog/eav_attribute',
            'entity_attribute_collection' => 'catalog/category_attribute_collection',
            'attributes' => array(),
        );
        foreach ($this->_category_attributes as $name => $options) {
            /* Override values provided by the defaults */
            $attribute_options = $default_attribute_options;
            foreach ($options as $k => $v) {
                $attribute_options[$k] = $v;
            }
            $entities['catalog_category']['attributes'][$name] = $attribute_options;
        }

        return $entities;
    }

}

in etc folder I have the config.xml contents:

<modules>
    <ProxiBlue_AttributeUseNormalFilterLink>
        <version>0.0.1</version>
    </ProxiBlue_AttributeUseNormalFilterLink>
</modules>

<global>
    <models>
        <proxiblue_attributeusenormalfilterlink>
            <class>ProxiBlue_AttributeUseNormalFilterLink_Model</class>
        </proxiblue_attributeusenormalfilterlink>
    </models>
    <resources>
        <proxiblue_filterlink_setup>
            <setup>
                <module>ProxiBlue_AttributeUseNormalFilterLink</module>
                <class>ProxiBlue_AttributeUseNormalFilterLink_Model_Mysql4_Setup</class>
            </setup>
        </proxiblue_filterlink_setup>
    </resources>
</global>

and in the sql fiolder I have the install script : mysql4-install-0.0.1.php contents:

$installer = $this;
$installer->startSetup();
$installer->installEntities();
$installer->endSetup();

Now you can adjust the filter template to use this attribute, and any category can be set to display the actual category link, and not work as a filter.

Copy the template catalog/layer/filter.phtml to your custtom theme folder, then adjust as follows: (note this has some other customization, so pull the bits you need)

<?php $category = false; ?>
<?php if ($this instanceof Mage_Catalog_Block_Layer_Filter_Category): ?>
<?php $category = Mage::registry('current_category'); ?>
    <?php if ($category): ?>
    <h2>
    <a class='level-top' href="<?php $category->getUrl(); ?>"><?php echo $category->getName(); ?></a>
    </h2>
    <?php endif; ?>
<?php endif; ?>
<ol>
    <?php foreach ($this->getItems() as $_item): ?>
    <li>
        <?php if ($_item->getCount() > 0): ?>
        <?php
            $link = $_item->getUrl();
            if(is_object($category) && !$category->getUseNormalFilterLink()){
                $filter = $_item->getFilter();
                if($filter instanceof Mage_Catalog_Model_Layer_Filter_Category) {
                    $linkCategory = mage::getModel('catalog/category')->load($_item->getValue());
                    if($linkCategory->getId()){
                        $link = $linkCategory->getUrl();
                    }
                }
            }
        ?>
        <a href="<?php echo $this->urlEscape($link) ?>"><?php echo $_item->getLabel() ?></a>
        <?php else: echo $_item->getLabel() ?>
        <?php endif; ?>
        <?php //echo $_item->getCount() ?>
    </li>
    <?php endforeach ?>
</ol>

Please see app\code\core\Mage\Catalog\Model\Layer\Filter\Category.php

It gets the categories using method protected function _getItemsData()

You can change its logic to return required category ID (say 476) when no category.

Example:

find $categoty = $this->getCategory();

add lines

if ($categoty->getId() == 'YOUR All Categories ID'){
    $categoty = Mage::getModel('catalog/category')
            ->load(476); 
}