[config] Onboarding flow with persistence (#1929)

## Summary
In collaboration with @gpeal: upgrade the onboarding flow, and persist
user settings.

---------

Co-authored-by: Gabriel Peal <gabriel@openai.com>

codex-rs/tui/src/cli.rs

@@ -54,10 +54,6 @@ pub struct Cli {
     #[clap(long = "cd", short = 'C', value_name = "DIR")]
     pub cwd: Option<PathBuf>,
 
-    /// Allow running Codex outside a Git repository.
-    #[arg(long = "skip-git-repo-check", default_value_t = false)]
-    pub skip_git_repo_check: bool,
-
     #[clap(skip)]
     pub config_overrides: CliConfigOverrides,
 }