Are the files you are trying to copy into the Vault SolidWorks files? And if they are do these files have references or are being referenced by other SolidWorks assemblies?
Regardless of what type of files, there is no command line set that I am aware of to do this. You can create your own program to do this if you so desire or you could drag and drop. The bigger issue is if they are referenced SolidWorks files, they all have to be added to the Vault at the same time and "Checked In" in the right order or else you will have a very large amount of files with errors. If you check in an assembly before the parts and sub assemblies, it doesn't know where those files are and suppresses them.