Update documentation (more than 95% coverage)

Some changes in this pull request aren't strictly documentation (i.e. how to use a method or class), but:

- Simplify documentation processing (e.g. excluding files in the RDoc task); or
- Hide certain methods and classes from the generated documentation with `:nodoc:`.

The latter is useful because there is a lot of information (e.g. `NMatrix::IO::Matlab::Mat5Reader` internals) that shouldn't appear on public API documentation. Also, I added or updated "real" documentation for shortcuts, NMatrix::IO modules and classes and others.

Another minor change that I did is removing `autoloads` in NMatrix::IO. Apart from a `FIXME` asking for it explicitly, the speed gain should be negligible and it improves the organization of the files (it's easier to know what's being required).

I sent a pull request to the sciruby.com repository with the docs generated with this pull request: [#6 Update NMatrix documentation](https://github.com/SciRuby/sciruby.com/pull/6).