Update all dependencies

[jonas-schievink]

This PR:

• Removes all patch sections from manifests
• Removes all stray Cargo.lock files from packages that are already in a workspace
• Adds workspaces to all template directories
• Replaces all "*" dependencies with the newest version
• Updates all other dependencies
• Adds #[allow(deprecated)] to pin.set_high()/pin.set_low() statements, silencing warnings that have appeared due to the digital::v1->v2 move in the embedded hal. This can be undone once a new nrf52832-hal version is released that includes https://github.com/nrf-rs/nrf52-hal/pull/116.

Depends on https://github.com/jamesmunns/nrf52-bin-logger/pull/1 Merged!

Closes https://github.com/ferrous-systems/embedded-trainings/issues/13

[jonas-schievink]

I've tested this locally and everything seems to work fine.

[jamesmunns]

LGTM! Thanks!