$ git clone /path/to/repo/*
Initialized empty Git repository in /path/to/file.ext/.git/
error: ‘/path/to/repo/file.ext’ does not look like a v2 bundle file
fatal: Could not read bundle ‘/path/to/repo/file.ext’.

Fortunately, it happened after I’d just done a serious site-wide rename of a bunch of files, and I decided to try cleaning the repository.

This solved everything:
$ git gc /path/to/repo

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