The I/O configuration was managed by enforcing the type of the arguments
to be `argparse.FileType`.  While this is a neat option for prototyping
a CLI, it leads to annoying bugs.

The main issues are due to the fact that the files are opened/created
during the argument parsing stage.
- First, this is undesirable as the output file is created too early: if
  the input is an invalid linking matrix, we still create an empty
  output file.
- Second, the file is opened, forcing the developer to explicitly close
  it.  It is better to manipulate files with context managers.

The variable name `matrix` was polysemous.  It was used to described
both the Python object holding the linking matrix
(i.e., a List[List[int]]), and the `.read()`-capable object representing
the input file.
The former keeps the name `matrix`, while the latter is now referenced
as `fp`.