Zend_Application will read and merge multiple configuration files when in a .ini file you specify an attribute like so;

config[] = path/to/other.ini

Zend_Tool currently doesn't honor this method, because it utilizes the config attribute itself. This forces a developer to not use the configs directories if he also uses Zend_Tool.

Simple enough to fix in Zend_Tool_Project_Context_Zf_BootstrapFile::getApplicationInstance

    public function getApplicationInstance()
    {
        if ($this->_applicationInstance == null) {
            if ($this->_applicationConfigFile->getContext()->exists()) {
                define('APPLICATION_PATH', $this->_applicationDirectory->getPath());
                $applicationOptions = array();
                $applicationOptions['config'] = $this->_applicationConfigFile->getPath();
    
                $this->_applicationInstance = new Zend_Application(
                    'development',
                    $applicationOptions
                    );
            }
        }
    }

To

    public function getApplicationInstance()
    {
        if ($this->_applicationInstance == null) {
            if ($this->_applicationConfigFile->getContext()->exists()) {
                define('APPLICATION_PATH', $this->_applicationDirectory->getPath());
                $this->_applicationInstance = new Zend_Application(
                    'development',
                    $this->_applicationConfigFile->getPath()
                    );
            }
        }
        
        return $this->_applicationInstance;
    }