Please, more detail! We can't really guess what you're talking about.
What files? What is "Command Mode"? What is user-dirs.dirs? I have never heard of that.
What does X11 have to do with NFS? Is that "Network File System/Server"? or a different NFS? And what is "A/C"?
What OS is this on? Fedora? If so (or if not) what OS and version?