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Project\Plugin versioning

I have a question about versioning.

I have two different installation of of Unreal Engine 4.13:
A) first one taken from Epics Launcher.
B) second one git repository of source code.

If I work on a plugin or a project on A version when I try to open my project/plugin in the version B I need to convert the project.

Can you explain me why Unreal 4.13 installed version is different from Unreal 4.13 git repository (branch release) version?

Regards