build.plat, hdl.ir: coordinate missing domain creation.

build.plat, hdl.ir: coordinate missing domain creation.

Platform.prepare() was completely broken after addition of local
clock domains, and only really worked before by a series of
accidents because there was a circular dependency between creation
of missing domains, fragment preparation, and insertion of pin
subfragments.

This commit untangles the dependency by adding a separate public
method Fragment.create_missing_domains(), used in build.plat.

It also makes DomainCollector consider both used and defined domains,
such that it will work on fragments before domain propagation, since
create_missing_domains() can be called by user code before prepare().

The fragment driving missing clock domain is not flattened anymore,
because flattening does not work well combined with local domains.