Improve repo clone UX with live progress and protocol preference

[hex2dec]

Summary

• stream native git clone progress to stderr while keeping stable text and JSON command output on stdout
• add a saved clone protocol preference with a first-use SSH/HTTPS selection flow instead of silently defaulting to HTTPS
• preserve auth tokens when saving clone preferences and harden unauthenticated integration tests against local machine config leakage

Testing

• cargo fmt
• cargo test
• cargo clippy --all-targets --all-features -- -D warnings

Closes #42