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Alternative to https://github.com/ostreedev/ostree/pull/2197
Python's (usually) zero-sized `__init__.py` files can provoke
us hitting the hardlink limits on some filesystems (`EMLINK`).
At least one Fedora rpm-ostree user hit this.
The benefits of hardlinking here are quite marginal; lots
of hardlinks can behave suboptimally in particular filesystems
like BTRFS too.
This builds on prior code which made this an option, introduced
in 673cacd633
Now we just do it uncondtionally.
Also this provoked a different bug in a very obscure user mode checkout
case; when the "real" permissions were different from the "physical"
permissions, we would still hardlink. Fix the test case for this.
558720e7aa