Rewrite BlackBox IO contract, replace _clock|_reset

The old blackbox behavior still emitted extmodules that have a
clk, reset pin and prepended all io's with io_ (ultimately). Most
verilog modules do not follow this distinction (or use a slightly
different name for clock and so on).

Thus, instead BlackBox has been rewritten to not assume a clk or
reset pin. Instead, the io Bundle specified is flattened directly
into the Module.ports declaration. The tests have been rewritten
to compensate for this. Also, added a test that uses the clock pin.

As a secondary change, the _clock and _reset module parameters were
bad for two reasons. One, they used null as a default, which is a
scala best practices violation. Two, they were just not good names.

Instead the primary constructor has been rewritten to take an
Option[Clock] called override_clock and an Option[Bool] called
override_reset, which default to None. (Note how the getOrElse call
down below is much more natural now.)

However, users may not want to specify the Some(their_clock) so I
also added secondary constructors that take parameters named clock
and reset and wrap them into Some calls into the primary constructor.
This is a better UX because now you can just stipulate clock=blah in
instantiation of that module in symmetry with using the clock in the
definition of the module by invoking clock.

PS: We could also back out of allowing any overrides via the Module
constructor and just require the instantiating Module to do
submodule.clock := newclock, etc.

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