cargo-machete: clean-up and integration into the check workflow.

[D-Stacks]

This PR:

1. Removes unused deps, as found by cargo-machete,
2. But Keeps false positives, which where manually tested to be required for compilation
3. Adds ignores for these false positives.
4. Integrates cargo machete into the checks workflow in github.

Future use:

To ignore a false positive, which one thinks is erroneously flagged by cargo machete, place the deps name under [package.metadata.cargo-machete] in the corresponding Cargo.toml file.

[D-Stacks]

probably out of date by now..