Upgrade most dependencies

[bwestlin]

Checklist

• [x] I have read the Contributor Guide
• [x] I have read and agree to the Code of Conduct
• [x] I have added a description of my changes and why I'd like them included in the section below

Description of Changes

Upgraded most dependencies as there are a lot of old ones, main thing I wanted to update was octocrab as we've been seeing some recurring errors that could be helped with a newer octocrab.

I have tested running manually as well as checked that cargo test passes.

[bwestlin]

@vojd Updated deny.toml as well