Maybe I'm misunderstanding JSON Schema, but the resolver seems to be adding directories onto it's resolver path as it goes down a relative path. If I have a 'project' schema that references a 'container' schema, that references a 'generic' schema, the references have to look like this to work, even with all files in the same directory:

project: "allOf": [ { "$ref": "file:schemas/container.json" } ],
container: "allOf": [ { "$ref": "file:generic.json" } ],

I've got a github project here because the example has to be a little involved: https://github.com/fleur/jsonschema-bug