When I start a new project, I want the public folder to be called web, and the app folder to be called private, as these are the defaults set up by ISPConfig for a new web site. "app" is hard coded into the phalcon-devtools. Additional project options are suggested --public-dir web --private-dir private. This might be substituted in the config.ini. As it is , I am just going to change the hardcoded values in my copy of the devtools scripts.