fix(commands): preserve root frontmatter metadata

[kriptoburak]

Summary

• Keep root Skill and agent metadata when nested YAML uses the same keys.
• Add parser coverage and update the install example to a current portable Skill that exercises nested metadata.

Anti-slop triage

• Classification: actionable-fix
• Evidence: triage: nested frontmatter overrides Skill metadata #3295 reproduces the incorrect description on 08106b0c3771ef5b4a5aa176acccd460e88b7325 with the public X Twitter Scraper Skill.
• Non-destructive review result: merge candidate

Verification

• cd rust && cargo test -p commands --locked
• cd rust && cargo test -p rusty-claude-cli --test output_format_contract skills --locked
• cd rust && cargo clippy -p commands --all-targets --no-deps --locked -- -D warnings
• python3 -m unittest discover -s tests
• scripts/fmt.sh --check
• python3 .github/scripts/check_doc_source_of_truth.py
• python3 .github/scripts/check_release_readiness.py
• git diff --check
• No live secrets, tokens, private logs, or unrelated generated churn are included.

Resolution gate

• Fixes triage: nested frontmatter overrides Skill metadata #3295. The regression test covers both frontmatter parsers.
• This PR is intended to merge.
• I did not merge or close remote PRs or issues from an automation lane.