fix(cli): prune stale groundwork entries without lock file

[pentaxis93]

Summary

• fix reconcile pruning so stale groundwork-managed skills/* dependencies are removed even when no prior install lock exists
• preserve safety by continuing to keep non-groundwork dependencies (and groundwork entries outside skills/*) untouched without lock evidence
• document the behavior change in the changelog

Changes

• updated prune_stale_managed_dependencies to treat an entry as managed when either lock history marks it managed or its dependency entry matches gh = "pentaxis93/groundwork" plus path under skills/
• added helper extraction for dependency fields from TOML dependency entries (inline table or table form)
• added regression tests for no-lock stale skill pruning and non-skills/* safety behavior
• synced the shipped-manifest order assertion in unit tests to include skills/systematic-debugging

Issue(s)

Closes #113

Test plan

• cargo fmt --all -- --check
• cargo test -p groundwork-cli prune_ -- --nocapture
• cargo test -p groundwork-cli update_prunes_stale_aliases_and_preserves_external -- --nocapture
• cargo test -p groundwork-cli

[github-actions]

I did not identify any regressions or actionable defects in the diff against origin/main. The pruning logic change appears consistent with the stated intent and is covered by focused tests for both removal and preservation cases.

Raw outputs: codex-review.md, codex-review.jsonl