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Create a git repo on-line (eg. github.com)
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Save your Unity project on your local filesystem
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Enable External option in Unity → Preferences → Packages → Repository (only if Unity ver < 4.5)
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Switch to Visible Meta Files in Edit → Project Settings → Editor → Version Control Mode
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Switch to Force Text in Edit → Project Settings → Editor → Asset Serialization Mode
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Save scene and project from File menu.
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Quit Unity and then delete the Library and Temp directory in the project directory.
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Delete everything but the Assets and ProjectSettings directory.
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Make your first commit. Open terminal and follow the next 6 steps.
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cd to/your/unity/project/folder
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git init
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git add *
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git commit -m "First commit"
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git remote add origin [email protected]:username/project.git
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git push -u origin master