You do not indicate which operating systems or languages are involved, so this makes it difficult for a particular job.
Git (and SVN and Mercurial, etc.) is great for version control, but system synchronization often requires more than version control. If you are a person like Python, you might like to read Modern Python Hacker Tools: Virtualenv, Fabric, and Pip . This suggests that synchronization is not only the code, but also your entire environment.
For simple file storage on two systems in sync, I recommend rsync . I use this for all kinds of tasks, both on the same machine, and for backup / synchronization of directories between machines. We have a client in SoCal, where we make a three-level backup strategy (2 on the site, 1 outside the site) from more than 5 terabytes of data, and it is based on rsync and rsnapshot .
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