docs(framework): README CLI section drifted from the real flags

[suleimansh]

The CLI block in packages/framework/README.md is missing shipped, user-facing flags:

• --serve and its family (--serve-install, --serve-build, --serve-port, --serve-path)
• --permission-mode and the new bypassPermissions default (fix(framework): default the CLI to bypassPermissions so the headless loop can build/verify #226)
• --max-passes, --dangerously-skip-permissions, --skip-preflight
• the doctor subcommand

It also describes --deploy as 'Narrate a deploy decision', but cloudflare/dokploy now do a real deploy (buildDeployTarget), which needs --cf-project or --dokploy-url + --dokploy-app (also undocumented).

Bring the README CLI list in line with --help.