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Under fsroot is another directory called test. Modified ContentTool code to access the test directory by passing "/test" as the identifier. This returns an id of "test". Note the problem in these identifiers: they can be passed back to the ContentHostingService to get the collections again. The path relative to the root need to be prepended.
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.