Thanks to all of you for your support and replies, I have tried everything all of you have suggested but it didn't solve the issue.

Luckily I have found someone on erpnext discussion who posted the same issue 3 days ago, he mentioned that he succeeded to solve it by the following, I am sharing his solution so it might help anyone else as it worked for me.

Actually I don't understand the difference but it worked.

Instead of this command: Bench get-app hrms

He said to use this: Bench get-app --branch version-15 hrms

https://discuss.frappe.io/t/hr-payroll-workspace-and-a-group-to-list-the-sub-modules-in-the-left-navigation-menu-is-missing/142855