Add --quiet flag, --json output, and config permission check

- Add global --quiet/-q flag to suppress non-error output
- Add --json flag to verify, snapshot rm, and prune commands
- Add config file permission check (warns if world/group readable)
- Update TODO.md to remove completed items

internal/cli/store.go

@@ -127,6 +127,7 @@ func runWithApp(ctx context.Context, fn func(*StoreApp) error) error {
 		LogOptions: log.LogOptions{
 			Verbose: rootFlags.Verbose,
 			Debug:   rootFlags.Debug,
+			Quiet:   rootFlags.Quiet,
 		},
 		Modules: []fx.Option{
 			fx.Provide(func(storer storage.Storer, shutdowner fx.Shutdowner) *StoreApp {