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Right, there's no handling of the extension conflict in this version. (I assume you mean the auto-identification is broken, not the readers themselves, since all the tests pass).
The long-term solution is to fix our low-priority readers with respect to this one, but that only really makes sense once this reader is merged into Orange (biolab/orange3#6791).
I'll think if there's a good temporary workaround, but for now you will need to manually select the reader you would like.
Caveat I interpreted your bug report correctly, otherwise more details please!
The addition of the HDF5Reader seems to break the currently active file readers.
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