As per #2560, passing in memory entangle files requires either absolute paths or prepending a ../ in order to run correctly with fud2. This is, of course, because fud2 executes in its own cache directory and the cider stage in fud2 does not know about the entangle files as a possibility.
The correct solution is probably to add a separate set of stage config values in order to make it pull in the files or use the appropriate path. Doing so requires a bit of conditional logic in the actual stage as this implies a set of addition flags passed to cider but not directly given by the user. This strikes me as a bit awkward, but I don't necessarily see a better option at the moment.