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Actually, in the linked case above I'm not sure that it was a deleted file: Mathlib is pointing to Batteries @ lean-pr-testing-6112 there, which was a mistake (it should have been nightly-testing). Regardless, lake really shouldn't hang!
See commit 3ad5449927085b63f4304a13d534105004783bdd from Mathlib for a repro.
I've reported this a few times on zulip, but we better have a tracking issue.
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