Adjust command hiding to use similar convention as hidden flags

plus breaking out "setup" portion of `App.Run` into its own method, cleaning up
some bits of the help templates, and allowing for runtime opt-in of displaying
template errors to stderr.

category.go

@@ -28,3 +28,14 @@ func (c CommandCategories) AddCommand(category string, command Command) CommandC
 	}
 	return append(c, &CommandCategory{Name: category, Commands: []Command{command}})
 }
+
+// VisibleCommands returns a slice of the Commands with Hidden=false
+func (c *CommandCategory) VisibleCommands() []Command {
+	ret := []Command{}
+	for _, command := range c.Commands {
+		if !command.Hidden {
+			ret = append(ret, command)
+		}
+	}
+	return ret
+}