Startup programs
How do I specify programs to run when Ion starts up?
Start them from .xinitrc, .xsession or whatever file you
started Ion from depending on your configuration.
How do I get these programs to show up in the frames they were previously in?
Short answer: you can't. Without session management support from both the applications and the WM it is not otherwise possible to uniquely identify windows and programs between sessions. Few applications and even fewer that should be of any interest to Ion users properly support session management. While there is a session management module for Ion1, Ion2 doesn't have one.
Long answer: In Ion2, it is possible to use winprops to map window classes to certain frames. This, however, will not work for individual windows and will affect programs started while Ion is running. See the section on winprops in the configuration manual for details on setting up the winprops.