After struggling with doing a basic filter pattern on my new Portfolio section, I found the clues I needed in this tutorial. Here is the basic function.

function index($cat = null) {


	
	if($cat == null) {
		// If no category chosen, just use the basic paginate function
		$portfolios = $this->paginate();
	} else {
		// Set basic params with conditions form $this->paginate
		$params = array(
			‘contain’ => false,
			‘fields’ => array(‘DISTINCT (Portfolio.id) as id’),
			‘conditions’ => $this->paginate[‘conditions’],
			‘joins’ => array()
		);

	
		// Add the search on the habtm relations table
		$joins1 = array(
			‘table’ => $this->Portfolio->tablePrefix.‘portfolios_categories_portfolios’,
			‘alias’ => ‘CategoriesPortfolio’,
			‘type’ => ‘inner’,
			‘foreignKey’ => false,
			‘conditions’=> array(‘CategoriesPortfolio.portfolio_id = Portfolio.id’)
		);
		$joins2 = array(
			‘table’ => $this->Portfolio->tablePrefix.‘portfolios_categories’,
			‘alias’ => ‘Category’,
			‘type’ => ‘inner’,
			‘foreignKey’ => false,
			‘conditions’=> array(
			‘Category.id = CategoriesPortfolio.category_id’,
			‘Category.slug’ => $cat
			)
		);
		array_push($params[‘joins’], $joins1);
		array_push($params[‘joins’], $joins2);

	
		$tmp = array();
		foreach ($this->Portfolio->find(‘all’, $params) as $row) {
			array_push($tmp, $row[‘Portfolio’][‘id’]);
		}	
		// Final paginate query with the Portfolio ID’s as ‘scope’
		$portfolios = $this->paginate(null, array(‘Portfolio.id’ => $tmp));
	}
	// Send var to the view
	$this->set(‘portfolios’, $portfolios);

}