Can a project have its own Line CLI settings?

Yes. Put a .line/settings.json in the project (and commit it to share with your team):

{
  "permissions": { "ask": ["bash(git push*)"], "deny": ["Edit(migrations/**)"] },
  "verify_command": "npm run check"
}

What a project can set#

• permissions.ask and permissions.deny, never allow, so a cloned repo can't grant itself permissions.
• verify_command
• hooks (these run only after you trust them with /hooks trust)

Your own ~/.config/line/settings.json still applies; deny rules from either place win.