All commands which read config (agent, services, and validate) will now
print warnings when one of the config files is skipped because it did
not match an expected format.
Also ensures that config validate prints all warnings.
Previously the logic for reading ConfigFiles and produces Sources was split
between NewBuilder and Build. This commit moves all of the logic into NewBuilder
so that Build() can operate entirely on Sources.
This change is in preparation for logging warnings when files have an
unsupported extension.
It also reduces the scope of BuilderOpts, and gets us very close to removing
Builder.options.