With shell integration disabled:

With shell integration enabled:

With these changes, when shell integration is enabled:

• the scripts in blue still run before the shell integration script
• thereafter, they run in the right order only when I explicitly set RCS and GLOBAL_RCS in the script because those are getting unset somehow
  

Even when shell integration is disabled, after the startup files have run, RCS and GLOBAL_RCS are unset.

Using setopt and unsetopt, I realized I should instead be checking the value of norcs and noglobalrcs

Last thing to solve for:

• the scripts in the blue box run before the shell integration script
• in order to run the scripts in order, they must be run again
• will this cause problems?
• is there a way to prevent them from running before?
  

Those are running before the script because our shell integration script is getting run as the .zshrc in the ZDOTDIR

So the real question is why are the user's startup files not getting run between the global ones.

That's because ZDOTDIR is used instead of home directory when ZDOTDIR is set.

So it's looking for if ZDOTDIR exists (it does) and is looking for zprofile etc in there (where it doesn't exist). so we need to copy files to ZDOTDIR that contain scripts that will run ~/.zprofile etc.

deferred handling RCS and GLOBAL_RCS to #147802