...and, indeed, these XML namespaces (MS Office and data types) and the CustomDocumentProperties tag are already known to be added by SharePoint, and apparently for well-established reasons (though not ones I understand not being a SP user): http://sharepoint.stackexchange.com/questions/30626/why-is-s...
From my bad experience, Git repositories (and I would go as far as to say any source code) does not belong on SkyDrive/OneDrive. This is OneDrive, not the newfangled Hailstorm by architecture astronauts[0].
I would recommend that everyone keep working copy of their source code outside of any form of syncing. If you must, create tape archives (or 7z or something) and sync them but never your working copy.
I've kept most of my Git repos in my OneDrive for the past few years. It's worked great.
As many others have said, OneDrive For Business is really more of a SharePoint + Groove document sharing / collaboration thing for businesses documents (as the name kind of implies). While it does similar things from a generic corporate user point of view, the mechanics are pretty different. OneDrive For Business works well for the same kinds of use cases that SharePoint does (mostly documents), but I wouldn't put source code in there.
Wonder if it would modify files in a git repository in the same way? Good luck recovering from that!