fix(core): revert to clap 3.0 API, allow deprecations, closes #3549

[lucasfernog]

What kind of change does this PR introduce?

• Bugfix
• Feature
• Docs
• New Binding issue #___
• Code style update
• Refactor
• Build-related changes
• Other, please describe:

Does this PR introduce a breaking change?

• Yes, and the changes were approved in issue #___
• No

Checklist

• When resolving issues, they are referenced in the PR's title (e.g fix: remove a typo, closes #___, #___)
• A change file is added if any packages will require a version bump due to this PR per the instructions in the readme.
• I have added a convincing reason for adding this feature, if necessary

Other information