D. Why do file permissions change when files are copied to research storage home folders and/or project spaces?

File transfer programs, including the Mac Finder and Windows Explorer, try to do  the best job possible matching permission when files are copies over. But since the operating systems typically are different between the source (your computer) and the destination (the storage on the compute grid), the programs attempt to match as best as possible. Of course, they often don't get it right. Please see our HOWTO document on Changing File Permissions.