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First thank you for taking the time to make a report.
There's definitively a tuning phase needed.
I've just committed an update that pass your example. fddaf71
Penalty for overall path length has been decreased, and to compensate penalty for base-name path length has been increased.
I'm not really sure how to best handle updating this. I'll probably emit a minor revision and people will have to do a npm update. I'll probably have to talk to the atom team too.
In the meantime feel free to hack the version in node_module if you want to test if you like new weights.
Thanks for improving Atom's file finder, it's something that's needed improvement for a long time!
I recently installed your improved version and ran into a case where I think it could be better. Here it is:
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