test.php

<?php

if (!empty($this->request->data('applications.companies_ids'))) {
                
                // Recupero gli ids delle aziende a cui l'agente si è candidato
                $companiesIds = array_diff(
                        $this->request->data('applications.companies_ids'), 
                        (new Collection($agent->applications))->extract('company_id')->toArray()
                );
                
                if (!empty($companiesIds)) {

                    $newCompanies = $this->Companies->find()
                                        ->contain(['Sectors'])
                                        ->where(['Companies.id IN' => $companiesIds])
                                        ->all();
                    
                    foreach ($newCompanies as $company) {                    

                        $application = $this->Applications->newEntity([
                            'agent_id'   => $agent->get('id')    
                        ], ['associated' => ['Companies.Sectors']]);
                        $application->company = $company;
                        $agent->applications[] = $application;
                    }

                }
                exit();
            }