change upgrade to only upgrade modified packages

[ashraffouda]

Description

only upgrade modified packages to reduce root disk usage size

Changes

upgrade was doing reinstall to all packages even if they are not changed which results in disk to ran out of space so we want to only reinstall the modified pkgs only

Related Issues

List of related issues

Checklist

• [ ] Tests included
• [ ] Build pass
• [ ] Documentation
• [x] Code format and docstring