Prefer CLI filter options to those in files

With the changes in 381b068f, it looks like we lost ordering information about how the exclusions and inclusions interleave. Internally, each group is consistent. Currently on master, I think all inclusions will be overridden by exclusions for the same value, regardless of the file/CLI/env ordering.

So concretely, overriding a project's `.rspec` file with CLI arguments doesn't currently appear to work.

This PR preserves the single Configuration reference from 381b068f, but keeps all the options ordered (`file_options << command_line_options << env_options`) for the filter manager. Seems to work well locally.

This affects releases starting with 3.0.0-rc1.