How to create the junction point for the git repository folder.

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Git

I have the following folder structure

C:\360\Source

- standard

C:\Main\Source

- custom


C:\Main\Source is the git repository folder. I want to create the junction point for C:\Main\Source folder so that custom should be linked to the C:\360\Source folder. I am using below command to create the junction point.

*mklink /j "C:\Main\Source" "C:\360\Source"*

But before creating the junction point I need to delete the original Source folder from C:\Main folder as you cannot create junction point with existing original location folder. Once the above command is executed the junction point will be created but my git will show the content of source folder deleted.

My question is how should I create the junction point so that I should not lose my git source folder files and after the creation of junction point the additional folder like standard should be ignored.

What I have tried:

I can not create the junction point by swapping the original location and target folder as original location is used by multiple developer.