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/restore.go

@@ -76,6 +76,7 @@ Examples:
 				LogOptions: log.LogOptions{
 					Verbose: rootFlags.Verbose,
 					Debug:   rootFlags.Debug,
+					Quiet:   rootFlags.Quiet,
 				},
 				Modules: []fx.Option{
 					fx.Provide(fx.Annotate(