I also experienced the problem with storing some git repositories on iCloud Drive. I call these files "ghost" files because the cloud icon is drawn with a dashed line. According to Apple these are files that are waiting to be uploaded to iCloud Drive. Here's what solves it for me though I am still researching a way to resolve it programmatically - i.e. navigating through the file system to detect these ghost files and then perform my process to get them uploaded. On the Mac I simply use Finder and navigate to the folder containing the ghost file that is waiting to upload. I right click and select the Compress command to create a .zip file of that ghost file. In only one case this was enough to trigger the uploading of the original since the ghost icon disappeared. In every other case it was not enough. In these other cases I would wait until the cloud outline disappears from the zip version of the original file - indicating it's been synced to iCloud Drive on the server. Then I delete the ghost file. Finally I unzip the zip file and it recreates the ghost file and nearly every time it syncs to iCloud Drive. If the zip file doesn't sync after a few seconds you could delete it and try it again. I had to do this once. If you want to be even more cautious you can unzip the compressed file and then check the contents against the ghost file. Once confirmed they match then just delete the original file as well as the .zip file and then rename the uncompressed one since it will have a " 2' added to the name. I've now done this about 40 times over the past few days while doing a lot of git repository synchronizations. It's a pain but it's never not worked. The real solution would be a utility script that could look for these ghost files in a hierarchy, like via the "find ." command, and then trigger this zip process. Unfortunately it would have to wait to conduct a second pass to make sure all the zip files have been uploaded before it would delete the problem files and then unzip the backups. Finally, it would have to do a third pass to confirm all the unzipped replacement files have been synced to iCloud Drive.