It is very simple. There is one repository per 10x10 tile. Each repository has two branches -- master (empty), Terrain, and Objects. Master is the default branch.
Therefore, you need to do this from the TerraGit home directory in your console:
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cd Terrain
cd *tile you cloned*
git checkout Terrain
cd ../../Objects/*tile you cloned*
git checkout Objects
If you want to develop, simply do this code inside the relevant tile directory:
Developing in /Objects/
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git checkout Objects
git pull
git checkout -b *newbranchname*
Developing in /Terrain/
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git checkout Terrain
git pull
git checkout -b *newbranchname*