Change handling of loadpath and mlpath.

- Option -I no longer handles loadpath, only mlpath. This is the same
  behavior as coq_makefile. Option -I-as is unchanged.
- Option -R no longer recursively adds to mlpath; only the root directory
  is added.
- user-contrib/ and xdg directories are no longer recursively added to
  the loadpath.
- theories/ and plugins/ are no longer recursively added to the loadpath
  when option -nois is passed.
- All the preconfigured directories are still recursively added to the
  mlpath though.
Add tool for fully qualifying Require statements.