I have files in my workspace that are either not in vault yet, or I have them checked out making changes. These files more than likely have some of our standard library components (i.e., fasteners, electrical parts,....).
If I open a file from Vault, I should get all of the files that are needed to open it. When I am done working on that file, if I close it and delete the local copy, the standard library components will not be available for the other files that I have on my workspace. That is when I get the resolve link dialoge.
Instead of deleting ALL of the files when I close the assembly, it would be good to NOT delete files from a particular directory. This could be done with a filter or from a list similar to the one you get when you "Check-out" an assembly.