update flake and rust dependencies

[Chaostheorie]

This is a naive update with minor adjustments for new APIs. Most changes are clap related because their macro naming has changed.

[Chaostheorie]

The only skipped dependency is rnix, it had a few breaking API changes that likely require a bigger refactor. I can try to tackle this in the new few days.

[Chaostheorie]

This also now contains a minor fix for #307 and #287, if required, this can be split into its own PR

[Chaostheorie]

Tested the PR locally, works fine. No regression appears to be present.

[Chaostheorie]

After an hour on a builder, nixos vm test failed, seems like activation CLI needs some more work:

vm-test-run-options-overriding> client # thread 'tokio-runtime-worker' panicked at /build/source/src/deploy.rs:493:37:
vm-test-run-options-overriding> client # called `Result::unwrap()` on an `Err` value: ()