make coqdep canonicalize paths from the command line

I'm not sure if having periods inside the 'as' is considered bad but this makes it work in coqdep the same way that it works in coqc.

- logical paths given to -R and -I should be split
  on periods.
- it also seems like giving an empty string should
  result in the empty path rather than the singleton
  path with an empty string as an identifier.