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.
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