Previously, we checked scripts in a separate run to work around mypy
not supporting multiple scripts with the same name. Since we have
fixed that issue, we can restore the original behavior.
We leave the --scripts-only option available, though I'm not sure it's
particularly useful and we'll probably eventually remove it.
We're now at the point where 100% of functions checked by mypy is
fully annotated; to avoid regressions, we're enforcing the requirement
that it stay this way. We still have a moderate amount of code that
is neither checked by mypy nor annotated, but it seems reasonable to
annotate that code at the same time as we get a chance to fix the mypy
issues in it.
This is implemented by using the --disallow-untyped-defs option in
mypy by default.