Use [patch] section to control local crate replacements

The nitrokey-sys crate poses a challenge in that upgrading it causes
build errors caused by linking against the system's nitrokey library
from multiple crates, which is not allowed. The exact cause of the
problem is unclear but the suspicion is that a bug in Cargo's replacing
logic is the cause of the issue.
To work around this problem, this change switches to using the [patch]
section for replacing crates with local copies instead of the [replace]
one.

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