Refactor cmd setup and remove deadcode (#29313)

* use `setup(ctx, c.Bool("debug"))` like all other callers
* `setting.RunMode = "dev"` is a no-op.
* `if _, err := os.Stat(setting.RepoRootPath); err != nil` could be
simplified

(cherry picked from commit e9b13732f3d3b5536e43bdfdb5757dbbf484d694)

cmd/keys.go

@@ -71,7 +71,7 @@ func runKeys(c *cli.Context) error {
 	ctx, cancel := installSignals()
 	defer cancel()
 
-	setup(ctx, false)
+	setup(ctx, c.Bool("debug"))
 
 	authorizedString, extra := private.AuthorizedPublicKeyByContent(ctx, content)
 	// do not use handleCliResponseExtra or cli.NewExitError, if it exists immediately, it breaks some tests like Test_CmdKeys