Changed .file.type to process_file
beginning to clean up poppr function
Simplified tabultaion of MLGs
Moved diversity calculations outside of if state
Changed printing scheme for poppr.all.

It will also now take a list of genind or genclone objects. The only
caveat is that the list should have names. Otherwise, it will just
print out numbers.
Updated and reran vignette.
updated poppr man page.