Properly canonicalize crate paths specified via --extern

Crates that are resolved normally have their path canonicalized and all
symlinks resolved. This does currently not happen for paths specified
using the --extern option to rustc, which can lead to rustc thinking
that it encountered two different versions of a crate, when it's
actually the same version found through different paths.

To fix this, we must store the canonical path for crates found via
--extern and also use the canonical path when comparing paths.

Fixes #16496