Git repository in OneDrive synced folder

OneDrive does not (yet!) support syncing files that start with periods, like the .git folder where the git metadata is saved to.

Because of this you are not seeing those items sync over OneDrive.

(This is only the case with old version of the OneDrive Client, I've created a new answer that reflects the current versions capabilities 8/2015)

Manual creating folder with name ".git" works, and ".git" appears on the onedrive server.

The OneDrive sync client now supports syncing folders that contain the period character within them '.' this should enable you to start syncing those git repositories automatically so long as they are within your OneDrive folder.

Get the latest version of the OneDrive Client and you are all set.

As of 6/27/2017, Version 2016 (Build 17.3.6917.0607)

OneDrive for business will support synching dotfiles (and dotdirectories) However, OneDrive is a VERY bad solution unless you add commit hooks to exclude files: https://support.microsoft.com/en-us/help/3125202/restrictions-and-limitations-when-you-sync-files-and-folders

Also, I dont know about how things would behave under race conditions. If there is more than one committer (inc automated stuff), it might not be safe.