How do I programmatically alter the links displayed in the main navigation menu?

The main navigation menu in the site I am currently working on has a lot of menus. I want to hide the disabled ones.

I figured out that it is rendered via the menu_edit_form form.

entity.menu.edit_form:
  path: '/admin/structure/menu/manage/{menu}'
  defaults:
    _entity_form: 'menu.edit'
    _title_callback: '\Drupal\menu_ui\Controller\MenuController::menuTitle'
  requirements:
    _entity_access: 'menu.update'

I could not locate the menu edit form from the above entry. I am thinking of a doing form alter but is there a better way to alter the links shown in the form and also how do we locate the form that is used to display the link.

I figured out how to do this.

The form actually resides at

Drupal\menu_ui\MenuForm

As this is an entity form it has to be set/defined in the annotation of the ContentEntityType 'menu'. This is where the form class is usually linked with the 'menu.edit' found in the routing file _entity_form entry.

However I could not find such an annotation at first. Then I finally figured out where this is defined

/**
 * Implements hook_entity_type_build().
 */
function menu_ui_entity_type_build(array &$entity_types) {
  /** @var \Drupal\Core\Entity\EntityTypeInterface[] $entity_types */
  $entity_types['menu']
    ->setFormClass('add', 'Drupal\menu_ui\MenuForm')
    ->setFormClass('edit', 'Drupal\menu_ui\MenuForm')
    ->setFormClass('delete', 'Drupal\menu_ui\Form\MenuDeleteForm')
    ->setListBuilderClass('Drupal\menu_ui\MenuListBuilder')
    ->setLinkTemplate('add-form', '/admin/structure/menu/add')
    ->setLinkTemplate('delete-form', '/admin/structure/menu/manage/{menu}/delete')
    ->setLinkTemplate('edit-form', '/admin/structure/menu/manage/{menu}')
    ->setLinkTemplate('add-link-form', '/admin/structure/menu/manage/{menu}/add')
    ->setLinkTemplate('collection', '/admin/structure/menu');

  if (isset($entity_types['node'])) {
    $entity_types['node']->addConstraint('MenuSettings', []);
  }
}

The above was found in the menu_ui.module. So I learned today that there is alternative way to define the entity form.

So based on the above findings and to answer the question - to alter the Menu edit form links I did the following

1. I proceeded to extend the MenuForm in my custom module
2. I added a hook_entity_type_alter in my custom module where I linked the new form with the route.

/**
 * Implements hook_entity_type_alter().
 */
function my_custom_module_entity_type_alter(&$entity_types) {
  $entity_types['menu']
    ->setFormClass('edit', '\Drupal\my_custom_module\MyCustomMenuForm');
}

and voila I could get the new extended custom form in the url instead of the old one.