If you want to use version control with MPLAB® Harmony, you should put your framework in a non-versioned directory and the project in a parallel folder.
For example, install the framework into: /Users/username/Projects/harmony/. Install the project into: /Users/username/Projects/ /firmware/ .X. Everything under /Users/username/Projects would go into the version control repository.
If you require development on two Harmony projects at the same time, consider whether it makes more sense to have two separate repositories of Harmony installations and respective projects or one repository for the mutual framework and one for each project. Two separate repositories containing the framework for each project (and the project in development) is the easiest to maintain and the most scalable solution.