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Fixed this by passing in the id String as well as a File to FSCollection constructor. This allows the id to be kept apart from it's File representation, though this could lead to inconsistency with the File form. Tested against getId(). Implemented and tested getReference(). Both work properly now.
Created FSResource. Implemented constructor, getId(), and getResource() very similar to those in FSCollection. Added and implemented getResource in FSHostingService.