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?
Fix incoming!
Thanks, @bcherny You guys are the best!
@michael-abdo , I'm running into a problem with permissions as well with the user defined ~/.claude/settings.json as well as settings.local.json too with new projects. Are you able to describe your process to get the ~/.claude/settings.json to work correctly? Do you have to copy those settings over to settings.local.json and then restart the claude session (effectively making the global user settings.json not work)?
Having the same problem, I thought that the config is gonna inherit but I have to re-approve or re-copy it everywhere on each new project