My Uni provides us with Box cloud storage and I use it more-or-less for everything and access files via the Box Drive, which is a virtual caching filesystems. For the most part, this works great as I am automatically synced and backed up across computers. (All mac/osx.)
The problem is with RStudio. I get streams of error messages about file conflicts. Others have noticed this too. I think the problem comes down to the caching of files in the .Rproj.user directory. In a large project where I was having 100's of sync conflict messages, I tried deleting this directory. I suspect it had grown to many 1000's of files because Box was constantly renaming conflicting files. I actually could not delete locally and had to go to the Box cloud web interface and delete it there. After deleting that directory, all of the error messages disappeared. I was able to open the project and work with rmarkdown files without problems.
I am wondering if there could be an option to clear the .Rproj.user directory after each session, or perhaps keep that directory somewhere else in the file system (like /tmp). (I don't think symlinks work in Box Drive.) This could be implemented in the project settings.