MIR: bump the version of dependencies

What

This MR updates the MIR dependencies.

Why

It is of paramount importance to update num-bigint from 0.3.0 to 0.4.6, disabling the default features, as it introduces floating point operations.

tezos_crypto_rs and tezos_data_encoding must be updated from 0.5.2 to 0.6.0, as they otherwise rely on the problematic num-bigint versions. Since these crates are being updated, it also seems like a good opportunity to update the other crates.