doc: remove git:// protocol, adjust nits in onboarding.md

A few nits found during onboarding session.

• git:// protocol is dropped on GitHub Refs: https://github.blog/2021-09-01-improving-git-protocol-security-github/
• Recommended way to update fork from upstream should be reset, not merge. It's less resource-consuming and more straightforward. Maybe there are other arguments for that.
• Example commit is replaced with a modern one. The main difference is absence of @ in commit message to avoid random pings afterwards. Refs: https://github.com/nodejs/node/pull/42718#issuecomment-1098204164