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Prevent root_dir option from being empty (#448)

* Prevent root_dir option from being empty

When setting root_dir to an empty string (as is done in the default rake
task config) this line previously caused root_dir to become an empty
array.

This in turn caused factories, specs etc not to be annotated.

This is just a quick band-aid on a larger problem. We have option
parsing spread out over many different places, with slight mismatches
like this in the assumptions made.

* Handle blank values & comma-separated strings in AnnotateModels.root_dir

These cases are currently handled (inconsistently) in the different
option parsing routines.

* Pass root_dir forward unmodified

The different cases are now handled inside AnnotateModels

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