Issue Title: Delayed Permission Inheritance in Claude Instance Configuration

Bug Description
I am using ~/.claude/settings.json to define global permissions for each new claude instance. However, it does not initiate the inheritance immediately when I create a claude instance in a new folder. Instead, I have to reach a command that allows me to accept to allow that command to always run which then creates the local settings (settings.local.json). Then only after I've restarted the claude instance does it reference the local settings and then pulls in the master settings. Am I doing this correctly? Or is there a way to immediately inherent the allowed permission as soon as claude begins?